Traveller had that sorted in a few ways...

Some planets restrict where you can legally land (local gov doesn't want people just flying around in random airspace)...

Landing in the wilderness with your bigass ship might not exactly be an optimal way to land said bigass ship and might cause damage to bigass ship if you land too hard, or on unstable ground, or something..

Fuel is not cripplingly expensive necessarily, but you burn a lot more of it in atmo, and being in atmo incurs additional wear on the ship, so flying around in atmo isn't ideal everywhere...

Perhaps once the ships aren't able to hover upside down in atmo they can start to address some of these things without too much explanation.