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I’ve created a fairly fleshed out, detailed FTL concept. Basically, you have a circular starship, with a ring of tungsten encircling that, held in place by an antigravity ring beneath it. The rim of the starship consists of a plasma window - basically superheated plasma held in place by a magnetic field. This plasma is made from a material that, when, strongly heated, emits radiation. This radiation converts ordinary matter into Negative Matter (so, matter with a negative mass). Once enough of the tungsten ring has converted into Negative Matter (and the amount needed is pretty small) an Alcubierre-style warp bubble is created around the ship, taking it to its destination at a speed faster than light.
For story reasons, I’d like it to be the case that these ships can only work in space - so a ship has to first leave the atmosphere of whatever planet or body it is on before it can fire its warp drive. Considering its mode of operation, is there any plausible reason why this could be?

SHORT ANSWER:

There are several obvious reasons why using a warp drive near a planet might be a bad idea in your story.

LONG ANSWER:

And here are some of the reasons:

The concept of the Kzinti Lesson first appeared in Larry Niven's novel Ringworld (1970) and refers to his story "The Warriors" in If magazine in 1966. It is phrased as:

A reaction drive is a weapon effective in proportion to it's efficiency.

https://scifi.stackexchange.com/questions/13044/what-is-the-kzinti-lesson-from-larry-nivens-ringworld1

Anyone who watches the takeoff of a large rocket from a safe distance should be able to appreciate why getting much closer to the takeoff would not be a good idea.

Long ago I read an article where a scientist dismissed the possibility of even slower than light interstellar travel. He chose what seemed like a reasonable size for a starship and calculated how powerful the rocket engines would have to be to have enough thrust to accelerate the ship's mass enough to build up a decent speed for interstellar travel, and then calculated if the ship was launched from Earth with rocket engines at full power it would exterminate all live on Earth with the blast.

Naturally he didn't think that maybe the starship would take off from Earth with the rockets working on enough power to lift the ship from Earth but much less than full power, or that the starship could have been built in outer space far enough from a planet that it wouldn't damage the planet.

But what about a slower than light or faster than light space drive which doesn't use a reaction motor?

My answer to this question discusses why a faster than light starship would be dangerous even if not equipped with missiles or ray guns:

How does one intimidate enemies without having the capacity for violence?2

You may have heard of the theoretical Alcubierre warp drive. I have read that a ship using that warp drive would accumulate matter and energy as it traveled, and when it turned off the warp drive that matter and energy would be discharged in a blast that would devastate any planet it hit.

If so, a starship using that warp drive would have to stop to discharge energy in interstellar space and restart several times during an interstellar voyage in order to preserve the destination. But a warship headed to another planet to destroy it would leave the Alcubierre drive on for the entire trip to built up energy for a blast to destroy the target planet at the end of the voyage.

And here is another thing to think about. Suppose that a starship uses its faster than light drive to actually enter the atmosphere and land on a destination planet. Suppose that the starship is travelling "only" ten times the speed of light, or only about 3,000,000,000 kilometers per second.

In order to shut off the stardrive within 1 kilometer of the desired position, within 1 kilometer of the surface of the destination planet, It would have to be shut off within one three millionth of a second. That is rather precision work. Can the star drive even shut off that fast?

Would precision of even 1 kilometer be enough? If the starship cuts off power 1 kilometer above the surface, it might fall 1,000 meters to the surface and crash and kill everyone aboard and damage the surface. If it cuts off power 100 meters above the surface, it might crash and kill everyone aboard. If it cuts off power 10 meters above the surface, the fall might kill some people and will probably injure many. If it cuts off power even 1 meter above the surface, there may be injuries and the passengers should complain to the management.

Suppose, on the other hand, that the starship shuts off the interstellar faster than light drive 1 kilometer farther than the desired position, and thus 1 kilometer below the surface. Or 100 meters, 10 meters, or 1 meter below the surface. What will happen?

Nobody can calculate what would happen since there is no theory for a fictional faster than light drive that is sufficiently plausible for calculating the details. It seems natural to predict an explosion. But what percentage of the destination planet's population would survive seems impossible to guess.

Suppose on the other hand that a starship uses its faster than light drive to take off from an inhabited planet. An inhabited planet would usually have an atmosphere about as dense as that of Earth's.

Why does the air glow red hot in front of space vehicles reentering Earth's atmosphere? because at first those vehicles are traveling many times faster than the air molecules possibly could. The air molecules can't get out of the way so they are slammed together and compressed against the air molecules beyond them. When a gas is compressed it heats up, so the space vehicles slamming into the atmosphere create super hot zones of gas ahead of them.

And if the heat shields of those space vehicles fail, as that of the Columbia failed, the vehicles are destroyed and everyone aboard dies.

Orbital speed in low Earth orbit is about 7.8 kilometers per second, about 0.000026 times the speed of light, and reentering vehicles would be travelling slower than that relative to the air.

A vehicle taking off from Earth at ten times low Earth orbital speed or 78 kilometers per second, or 0.00026 times the sped of light, would have much hotter zone of gas ahead of it, and once the vehicle entered outer space it would take some time for that gas to disperse.

A vehicle taking off at 100 times orbital velocity would be travelling at 780 kilometers per second or 0.0026 times the speed of light. A vehicle taking off at 1,000 times orbital velocity would be travelling at 7,800 kilometers per second or 0.026 times the speed of light.

A vehicle taking off at 1 percent of the speed of light, or about 2,997.92 kilometers per second, would be travelling at 384.34 times orbital velocity.

A vehicle taking off at 10 percent of the speed of light, or about 29,979.2 kilometers per second, would be travelling at 3,843.4 times orbital velocity.

A vehicle taking off at the speed of light, or about 299,792.458 kilometers per second, would be travelling at 38,434.929 times orbital velocity.

A vehicle taking off at 10 times the speed of light, or about 2,997,924.58 kilometers per second, would be travelling at 384,349.29 times orbital velocity.

Clearly a space ship taking off using a faster than light drive would have to use only a tiny fraction of its speed while within the atmosphere in order to avoid smashing itself against the equivalent of a brick wall made out of super hot plasma. A spaceship capable of travelling through the atmosphere at even a few percent of the speed of light without destroying itself shouldn't have to worry much about enemy ray guns or atomic missiles.

In Star Trek IV: The Voyage Home (1986), Kirk, aboard a captured Klingon ship in Earth's atmosphere, detects a whaling ship headed for their whales, and orders:

KIRK: Full power descent, Mister Sulu.

SULU: Aye sir. Full power descent.

And later, while still in Earth's atmosphere:

[Bird-of-Prey bridge]

KIRK: Well done, Mister Scott. How soon can we be ready for warp speed?

[Bird-of-Prey cargo bay]

SCOTT: Full power now, sir.

[Bird-of-Prey bridge]

KIRK: If you will, Mister Sulu.

SULU: Aye sir, warp speed!

And naturally there has been some criticism of those scenes because of what travelling at impulse or warp drive within Earth's atmosphere would do to the Klingon ship and to Earth's atmosphere.

I remember a story where a jet fight pilot travels back in time to World War One. His plane's missiles can't find any other jet planes to track and hit, so they are useless. But when his friend is shot down by the Mauve Margrave or Pink Prince or other version of the Red Baron, he finds a way to strike back. He swoops down low over the airfield of the Crimson Count or Dark Duke or whatever at high speed and the air turbulence he causes is like a tornado, wrecking buildings and tossing around fragile planes and men.

So if a starship should travel horizontally in the atmosphere at ten times or a hundred times the speed of a jet fighter, let alone at what would be a high speed for the starship, it would likely cause a lot of damage.

And also consider that a star drive would likely create a bubble around the starship where conditions are changed and faster than light travel is possible. Even a slower than light anti gravity engine would probably create an anti gravity bubble around a slower than light space ship. Any such bubble around a ship would affect all of the matter within the bubble, not just the ship.

So if that bubble around the stars ship is a few times the dimensions of the starship, the starship would take some earth and rock and air with it every time it turned on its engines and took off from the ground of an inhabited planet. And it would take that earth, rock and air with it and deposit it on the landing field of the habitable planet it landed on.

So what if the bubble around the starship has a radius of 100 kilometers, or 1,000 kilometers, or 10,000 kilometers, or 100,000 kilometers, or 1,000,000 kilometers, etc., etc.?

If the starship turns on its faster than light engines while in the vacuum of interstellar space, or even the slightly more dense interplanetary space, it won't matter how large the bubble around the starship is. It will only carry a small amount of matter and energy caught inside the bubble when it is turned on. Unless, of course, like an Alcubierre warp drive, the bubble picks up all the matter and energy it encounters in interstellar space.

But if the starship turns on its faster than light engines while sitting on the ground of a habitable planet, its bubble of altered space/time is likely to take away a chunk of rock and a volume of air with it.
If the starship's bubble takes away a large enough volume of air, the air rushing into the new vacuum could have hurricane force or tornado force or many times greater force.

If the starship's warp bubble takes away a large enough volume of rock, the planet will be too deformed to maintain that altered shape with a big chunk taken out, and it will reform into a new and somewhat smaller spherical shape. That will involve extreme geological events like super earthquakes and super volcanoes erupting.

And if the starship's bubble is large enough to enclose the entire planet, the starship will drag the entire planet with it into the destination solar system.

Therefore, it seems to me quite easy to imagine an imaginary interstellar drive that would be quite dangerous to a planet. So planets with knowledge of that interstellar drive would require that all starships turn off that interstellar drive and use some other type of space drive to land or take off. Or maybe require the passengers and cargo to transfer to interplanetary ships operated by the local government while still far from the planet.

And the local planetary defense force would probably be prepared to instantly destroy any approaching starship which violated their rules.

And also see this question and its answers:

What realistic way could limit an FTL drive to only travelling between stars?3

and:

What would happen if this FTL drive type concept were used in an atmosphere?4

Plasma is pulled by gravitational tidal forces. These tidal forces on a ship at rest are negligible, but if the warp field is stretching the frame of the ship, then from the planet's frame, the ship is no longer a hundred meters long, but it is stretched across 100s of thousands of kilometers making these tidal forces of gravity more extreme the faster you go. So, if you fly too close to a planet, the plasma will be pulled inside of it's field to have a disproportionate amount of plasma facing the gravity source. This could cause a variety of effects depending on how you envision your ship working such as causing your ship to be pushed toward or away from the planet, or causing it to go into an uncontrollable spin that rips it apart.

If you want ships to be able to get closer than the outer limits of the gravity well, consider that moving through an atmosphere at more than a few thousand kph can incinerate pretty much anything. Trying to fly through an atmosphere at warp speeds will experience the relativistic baseball affect as per the most commonly cited meem here on world builder: https://what-if.xkcd.com/1/

The traditional answer to this question is "FTL drives don't work within gravity wells", which is sometimes justified by saying that they require a region of "flat" spacetime to operate reliably. If you're within a gravity well (i.e., spacetime is significantly perturbed), then they become dangerously unreliable and can self-destruct, shoot you off in random directions at random (superluminal) speeds, etc.

If you're specifically looking for a reason why your drive would only operate in vacuum rather than banning it from gravity wells (so, e.g., it would be just fine within the gravity well of an airless world), then a very likely explanation would be that the plasma generated by the drive (and quite possibly also the negative matter, depending on its characteristics) would interact with any atmosphere (or other matter) it came into contact with, cooling it or otherwise interfering with the drive's operation, thus it must be used in a (near) vacuum to prevent such interference. In this case, trying to use it in atmosphere would simply prevent the drive from successfully "igniting". Or, if you decide that your negative matter is actually antimatter or something similar, it could lead to a catastrophic explosion if the startup process proceeds far enough to generate significant negative matter before shutting down.

Let's talk about fence posts

Have you ever driven a fence post into the ground? You betcha! You get one of those cool tubes with handles and bang! pound that sucker right in.

Now, I want you to keep that in mind as we talk about magnets. (Heh, you're going to love this. Trust me.)

A big-ol' magnet is resting against a block of iron. The magnet is the Earth and you want to separate the iron (your rocket) from the magnet. The pulling force of your arm is similar to the pushing force of the rocket exhaust. Why is this important?

Because you said your FTL drive creates negative mass!

Not much, but it's there!

You have that magnet and block of iron far enough apart that, at rest, the magnet doesn't pull on the iron (ship in orbit), but you just changed that block of iron into another magnet with the opposite pole pointing toward Earth!

Bang!

Your fence post (space ship) was just pounded a couple of feet (with an appropriate crater) into the ground.

Yeah... fence posts...

No one in their right mind would activate a negative-mass-inducing engine within the gravity well of a planet. You might have trouble activating it within the orbit of Mercury. Bang! It might cause a cool solar flare.

BTW, I recognize that I'm treating negative mass like the opposite pole of a magnet. Technically, two positive masses attract and two negative masses would attract. Opposing masses should repel (the opposite of a magnet). That's not as cool as my fence post metaphor, but it's worth noting. The repulsion would cost your your navigation completely. It's the same bang! but it's more like a bullet from a blunderbuss than two magnets.

But I wasn't willing to walk away from my fence post metaphor. Sorry.

"basically superheated plasma held in place by a magnetic field"

That's your reason right there. Do that in an atmosphere, and the plasma ring will be massively disrupted, leading to a uneven matter conversion. This, in turn, will ensure that the warp bubble is itself warped, the consequences of which can go from the inner volume being flooded in hard radiation from the asymmetric Alcubierre boundary (perhaps survivable, though, so in an emergency you might just go for it), to the warp bubble actually pulling apart whatever is inside - you do go FTL, but your feet go just a teensy bit faster or slower, resulting in you being messily ripped in shreds. The warp bubble continues resonating like a bell, pulverizing everything inside and reemerging at destination with a cargo of broken tech and bleeding corpses, promptly decompressing explosively since the ship's structural integrity has been compromised.

So, you don't go FTL while in an atmosphere.

You are trying to make a negative mass area by converting a tungsten ring. Having so much air inbetween the ship and the ring you are converting has consequences on this process.

This would mean that on planets without atmosphere your ships could travel.

Alternatively or additionally, gravity could risk the field being pulled out from the front of the ship as the negative matter cannot be carried by antigrav. This means you need a stable orbit or outer space where the negative matter will fly along with the ship to function, preventing use too close to a planet's atmosphere.