The ships can land and take off at least some of them can but they don't fly around in the atmosphere they just go up and down they're either on the ground or they're in space but they can't really manoeuvre.

Except for that one episode of Voyager where they just kind of forgot about that, but I think that was hand-waved away by saying that they just made the shields into a bubble and so essentially from the air's perspective the ship was a sphere. That's apparently what the shuttlecraft do too, which is why they fall like a brick whenever they're shot down.