Actually I don't think that Star Trek "flying box" shuttle pods are that bad. On earth a lot of our vans are simply boxes on wheels because it's cheaper to make them that way and ignore areodynamics. I can imagine the managers at the Acme Budget Shuttle Pod factory saying, "Who cares if the hand wavium drive gets crap mileage in an atmosphere? Just so long as our sticker price is less than the competition!"

Of course that people would actually pilot the shuttle pods is laughable.