I think it's an artifact of the specific western (especially American) culture that we live in, and how over the last 80 years or so we've had relentless marketing that seeks to amplify boudaries between genders. It's a pretty common and effective approach to sell things by way of making people feel inferior to their peer group. ... "you're a woman, women have smooth skin. Is your skin smooth enough? Try our exfoliating lotion!" ... "you're a man, men like football. Do you show others you like football enough so that they're sure you're a man? Buy this ugly-ass jersey and solve that problem from a block away!"
So you end up with some (a lot) of people who have bought enormously into a completely bogus interpretation of what gender even is, provided to them by an extremely well funded, pervasive army of marketers, intent on propping up that bogus conception to sell everything from lipstick, to pickup trucks, to bacon, to real estate. "This is who you should be, let us sell you something to help you embody that image"
Then along comes one of us .. living, breathing, undeniable proof that not everyone buys that BS. The internal question becomes unavoidable "is there something wrong with my understanding of my place in the world, or is there something wrong wth this other person?" It's the rare person who will extend their understanding of the universe to include us, and it's far more likely we will be instinctively interpreted as a threat.
The are of course a lot more aspects to it, but I do honestly think this is where a lot of the knee-jerk hostility towards non-gender-conforming people.comes from, and also why you tend to see a lot more of it in the older generations than the younger ones.