As far as I know all manned aircraft pilots in the US military are commissioned or warrant officers. I think it makes complete sense that you would want a pilot that was specifically trained for whatever missions you were going on. Someone whose sole focus is on flying but can adapt in a pinch and has management skills to offload some of the work from the commander and XO.
In a normal aviation company there are two platoons of pilots and almost all of those are warrant officers and a platoon leader who really just manages the other pilots.