Well, in TOS, the Enterprise did fly thru the Earth's atmosphere. It was after an accident that threw the ship back in time, to around 1967. It was intercepted by an F-104, and when they put a tractor beam on it, the F-104 started to break up. They beamed the pilot onboard, and complications ensued….For instance, the Enterprise is designed for interplanetary travel...not atmosphere penetration, as has been show many times. That's what the shuttle is for.