Bastardeux - a good question! The crux of the matter is that the RAF think that carrier Air Power is Air Power and should be done by the RAF. The RN believe that carrier Air Power is Naval Power and should be done by the RN - it's all a matter of perspective.
Interestingly the use of Apaches from Ocean/Illustrious provides the RN with a bit of a quandry. At the moment on one hand they are saying that it is a great capability and no issue with army crews doing it yet at the same time saying that only RN pilots could fly fixed wing from the carriers. It could look a little like their problem isn't with the concept but with the RAF and some sort of perceived failure if the loss of FW in the FAA is long term.