There are different approaches to naval aviation. On one end is the canadian approach, where the helicopters living on ships are run by entirely airforce crews. On the other is the American/Russian total separation of branches, to the point that navy pilots don't even call themselves pilots (Tom Cruise played a "naval aviator"). In the middle are solutions like the Australians, where all pilots are trained by the air force and are then transfered to naval aviation squadrons for type training.

All these countries have very different military cultures between air force and navy. Navies, people who drive ships, generally have more ridged rank structures. Airforces, groups that fly aircraft, delegate authority according to job descriptions. There are historical and practical reasons for this, mostly linked to minimum team sizes, but safe to say the two cultures can conflict. Keeping some degree of separation reduces conflicts and increases cooperation/safety.