Count,
I absolutely would not disagree with you that "the best of the best" (or more accurately, the best of the people we persuade to apply) should be in the cockpit, and no one is suggesting quotas based on population make-up. However, unless you believe that some part of the population is likely to be better at flying, the fact that your recruited population does not match the make-up of your overall population implies something.
It might imply that your recruiting efforts are poorly targeted, it might imply that your selection process is inherently biased or it might imply that something further up-stream (education for example) is out of whack. If it's the latter (and the RAF clearly believe that in this case based on the article) you have two choices - keep a system that doesn't take this into account or attempt to develop a system that will select based on inherent ability regardless of educational background to that point.
The best explanation I've ever seen of this was a big brother and a little brother watching a sports match over a fence with equally sized stools - "equal opportunity" is equal opportunity to see the match, not the same sized stool.