I sort of see your point but think if you are an identifiable minority within a group, there actually is a place for such sub groups. You are part of a smaller band and the comraderie from belonging to a small group feels good.
eg I think groups/clubs or organisations like The Tailwheel Pilot's Association or a Gruman Pilots Group or the Goldfish Club or whatever, makes perfect sense. Not so much 'the nose wheel pilots and navigators association' or 'the pilots who have never ditched a plane yet club' or 'the honourable group of fixed wing owners'.
Most pilot's are male by a big margin - why not a female pilot's group? Female pilots aren't common. Doesn't make them better or worse, just makes them a smaller group.
If most pilots were female then I reckon a male pilot's organisation would be fine. If that was how it was, I would probably want to join! not for any reason other than appreciating and revelling in that I and my fellows are different from your typical pilot.
I think we sometimes try and make simply acknowledging separatedness and enjoying the comraderie of that as more philosophical and political than it needs to be. Nothing to do with with racism or equality - a lot to do with enjoying being out of the run of the mill.
If female pilots become much more common I would suspect the various female only pilot's clubs or organisations would fade away. Until then - why not?
My 2c