In the US at least, Air Force officer ranks match the Army and Marines. Sci fi tends to use those ranks for ground fighting teams.

Ship structure makes sense for a large ship. There is no similar aviation structure, the guy ultimately in charge is the aircraft is the pilot in command, generally the one flying the aircraft.

Some technical terms make more sense too. A hull is watertight, it translates well to a ship in space. A fuselage is describing the shape of the main body of an aircraft.