I think I remember Voyager flying through Earth's atmosphere in
this episode and being shown on the evening news. The ship was caught on video gliding gracefully through the clouds.
Alternatively it was Generations (I think) where Enterprise most certainly does NOT fly. Granted it flew and landed in other times, but that one sticks out as a "not so much" moment. It wasn't meant to fly in that scene for reasons other than not being aerodynamic but...anyway.