This is one of the aspects of human existence which is ironically as difficult to sort out as it is, BECAUSE humans are as intelligent as they are, can communicate with words, and can and have set up vast complex physical and social structures, to organize their lives around.
Something I suggest for consideration, is that there is a real difference between how people act and react to things, and what people tell themselves and others about those things. And that honest people can and do make big mistakes, when they are trying to understand themselves, every day.
And on top of that basic confusion, comes the fact that once someone has come to ONE conclusion about something, they will often go on to build an entire edifice of linked deductions, policies, and automated reactions (i.e. habitualized behaviors) on those initial conclusions, no matter how confused or obviously unreliable or wrong those initial conclusions were.
Possible example:
A male interacting with an especially effeminate male, finds that his previously established reactions are causing him to be angry/frightened. What I’m thinking of with this, is that if you get into the habit of beginning to be sexually drawn to someone else, based on how they move or speak, and then come upon someone who moves and speaks that way, but is of the “wrong” gender, you might get angry or frightened in the same way you would if you discovered that something that appeared at first to be a friendly cat, was actually some other furry wild creature, which you knew to be dangerous.
The reaction by itself, has zero to do with prejudice, or superiority of one person/creature over another, it’s just a natural reaction to discovering that the existing systems the person had in place within their lives, didn’t prepare them to deal with the situation at hand.
From that “foundation” of a startle-response reaction, and entire set of rules, actions, social structures, philosophies, and so on, might be built up, all ultimately to make the person feel better about their startle response.
Once all the "solutions" to the original events are in place, since they are often based on lack of thought, rather than careful reasoning, they will become recognizable "problems" in and of themselves.
More talk ensues, to explain why it is or isn’t really alright to go with or reject the first reaction to the fight-or-flight instinct, and entire cultures and religions can be constructed around almost nothing.
But at the bottom of it all, no intellectualization can override the very real and normal reaction that people have when they are startled. So all of the “solutions” are renewed and rededicated, over and over again.
Even some of the modern attacks on the “bad” ideas for how to deal with the startle response, can themselves cause problems. Some people have made up an alternate false explanation for the startle response, trying to fight the “lets declare that the startle response is a magically wise proof that effeminate men are bad,” by even more idiotically declaring that “having the startle response at all, is proof that you are defective at your core.”