Of course everybody is not "equal" in every sense. If that were the case, I'd be as great a scientist as Newton, be able to give a speech as well as Winston Churchill, tell jokes like George Carlin, write a novel like Mark Twain, run a company like Steve Jobs, be able to play basketball like Michael Jordan, football like Brett Favre, and hockey like Wayne Gretzky. Given that I can do none of those things as well as all those guys, it's safe to assume we're not all equal, at least not in terms of talent or ability.
On the other hand, there's the popular civic ideal that "Everybody should be treated equitably under the law." I like this idea. In theory, it's 100% fair. It ostensibly allows for a level playing field so all comers can achieve according to their own individual talents and abilities.
When the idea of "equality" was promoted in the US Declaration of Independence, it was quite a revolutionary concept. Western society in that day was still dominated by monarchs, aristocracy and clergy. The idea was so revolutionary, in fact, that it's taken over 200 years for us to deal with it, and we're still trying to work it out. Back in the early days of the United States, only male, Caucasian landowners enjoyed the rights of full citizens. It took over 90 years for blacks, and then women to achieve voting rights, let alone the right to equal pay, equal opportunity, equal treatment under the law, etc.
I can see why its necessary to debunk nasty myths and vitriol directed toward these people, but its not really clear what your post suggests.
Sounds to me like the OP is sick and tired of the "PC police" telling him he has to respect queers and trannies as equals, but it's not OK for him to act like a naturally dominant, red-blooded man instead of an emasculated metrosexual as men are so often portrayed in our culture. He's asking why we so-called skeptics don't apply our critical attitude toward addressing those issues.
Is this a correct (if crudely-stated) assessment? Please feel free to call me out if I'm being presumptuous.