Anything larger than gunboats shouldn't land on planets unless it's an emergency as they lack the atmospheric equipment and designs to do so safely.
Realistically, ships should be constructed in space docks where no atmospheric flight capabilities are required to maximise their effectiveness in space. But obviously in Freelancer this is a different case, where capital ships would moor using mooring fixtures and use space elevators for loading supplies and personnel.
Oh, and Freelancer was never designed to accommodate atmospheric flight (eg entering planetscapes). So Digital Anvil just decided to make your ship go poof when you hit one.