I think a far better question is why do we have commissioned Pilots? The argument that they were the ones who carried the nuclear option does not hold water today. THe NCO pilots in the AAC flying Apache are, I think you will agree, doing a fantastic job (I speak from personal experience of these fine people). The Battle of Britain would not have been won without the heroism of NCO pilots.
So, yes, lets stop this elitist rubbish and reintroduce non commisssioned pilots and Navs. I think the idea of all commissioned crew is, quite frankly, rediculous, needless and bloody expensive. A percentage of non commissioned flight decks would also shrink the pyramid as the RAF would have to stop 'inventing' careers for all those on ground tours.
As to different perks based on rank, it's the way of the world and we are not nearly as bad as the Private Sector. If you make everyone the same then there is no incentive to better yourself. Plus, if I am expected to take on a far heavier workload and more responsibility than a SNCO, I have every right to expect a better 'package'.
I take issue with the fact that a SNCO with 20 years experience automatically makes a better commissioning candidate than 'airfix boy'. Some (not all) are very fixed in their ways, reluctant to change and have an approach not unlike some Shop Stewards I have met (the sort who use childish jibes like Airfix Boy). The best SNCO's I have ever had the pleasure of working with have not needed membership of the Officers Mess to make their presence felt.