As in most mainstream religions it is a "sin" (why, I've always wondered, and "because the LAWD said so" isn't a good enough answer for me) to wear a woman's clothes or behave as a woman, I'm pretty sure it is a socialized trait and not something that is instinctive. While many of the filled-with-hate religious people do act like Neanderthals, I can't accept that this is something that predates organized religion. This is another one of those things that stems from ignorance and forced ignorance, in which because this is a "sin", you're expressly forbidden to ask why or even explore why - it's taboo, you know, and the LAWD won't like it if you ask questions.

Simple enough test: take 10 babies under the age of 1, dress half them all as the opposite sex, stick them in a room and watch what happens. Do this over and over, and also do a control group where they're dressed "gender appropriately" a few times as well. Observe behavior. Do any of the babies start trying to kill the crossdressed ones? As an observer of behavior in young children, I've never seen this sort of behavior at all, not that I have replicated this exact experiment. But if it is indeed instinct, the non-crossdressed babies will start trying to kill the crossdressed ones. I just don't see that happening.

It takes years of socialization to build up that sort of hate, and babies haven't been exposed to it yet.