So although no work is being done on the aircraft (ie. its kinetic and potential energy remains unchanged) work is being done on the air
It's not strictly true to say that no work is being done on the aircraft. The engine does work on the aircraft, and if thrust equals drag, the aircraft does work on the air at the same rate. Thus the energy of the aircraft doesn't change. If you were to consider the aircraft climbing instead, thrust exceeds drag and the engine does more work on the aircraft than the aircraft does on the air. Thus the aircraft gains potential energy.
and therefore energy from the fuel is being consumed in proportion with the rate of change of momentum.
Fuel is consumed in (approximate) proportion to the work the engine has to do on the aircraft in either of the above cases.