In the US Air Force, aviators generally — though not always — command aviation units.  (Aviators do sometimes command non-aviation units, but even those units are often support elements to a flying mission.)

In the Navy, though, command above a certain level requires you to drive a boat.  So that’s what fighter pilots (“Naval aviators”) do.

The Navy Times notes new commands have opened up for aviators working their way up the ship command system.  Apparently, aviators often serve as second-in-command of a carrier, then command a non-carrier vessel, then return to command a carrier.

Of course, the article also notes that giving aviators these commands eliminates more slots from the Surface Warfare Officers — the guys whose actual jobs is to command the boats.