Why is it that humans tend to hate things that don't actually cause harm, like homosexuality, criticism and multiculturalism?

This is easy . . . Environment and Experiences.

In other words, people are "Raised to Hate" .  We watch our parents and our peers for social cues . . . If more parents actually cared they would fully understand this and make the change in themselves first (remembering they are fighting against how they were raised).

It is as easy as NOT teaching our children to hate things that are different them in race, color, sexual preference . . . Etc.

Many people tend to dislike things that are "different" or counter to their beliefs.

We've tried multiculturalism in this country, and it works 95% of the time. The other 5% of the time is snafu, and sadly outweighs the good. It is a very dirty word here now, and contributes to community friction in all sorts of depressing ways.

The 12 Monkeys
There was a group of scientists that wanted to run a social experiment with monkeys. They grouped 6 monkeys in to a large round room, with a ladder in the middle of the room, and closed them inside for observation.

After sometime a hatch in the ceiling would open up and lower a banana on a piece of string above the ladder. The scientist would wait for one of the monkeys to notice the banana and begin to climb their way up to reach it. At which time a ports in the walls would open and spray the other 5 monkeys with water from fire hoses. 

The scientists repeated this process until the monkeys no longer went for the banana on the string.

After sometime, they removed one of the monkeys from room and replaced it with another that was unfamiliar with the room. Again they introduced a banana on a string an waited for the new member to approach the ladder, but as it did the group of 5 monkeys jumped the new comer and beat it viscously.

One by one each monkey was replaced by another new member, that underwent the same trial,  however none of them are ever exposed to the water from the hoses.

Never the less, after the entire group is comprised of new members they never again attempt to climb the ladder.

Because as far as they're concerned, that's the way its always been around there.

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Sometimes people just don't know any better because all they see are the consequences of trying to stand out. Not saying thats why everyone hates but one of the reasons.