*sings* Why can't we be friends, why can't we be friends?
Because bob sincerely believes in X, and lucy sincerely believes in Y, and johnathan sincerely believes in Z, and when you put them all in the same room, they see differences instead of similarities. Humans sincerely feel a deep rooted desire to belong, and there are few places of belonging more powerful than ones founded on absolute faith.
The man who believes that homosexuality is a sin with absolute faith, cannot be wavered from his or her position, because you cannot convince this person who has spent
years doing what they sincerely believe is absolutely right, to dare question it. Because the mere act of questioning it sets them upon a moral precipice they cannot turn back from, which according to their own beliefs leads to torture and damnation in equally eternal measures. When you have generations of people brought up to behave like this, it becomes very hard to break them away--because now you're attempting to convince an individual human to potentially not only lose group association to their faith, but to their own
families who may sincerely worship this faith.
We can't be friends because the same intelligence that grants us the capacity for reason also orchestrated complicated social narratives on several levels that give us comfort and a sense of belonging. We're social animals, and social animals form packs. Wolves do it, dolphins do it, and humans are no exception. We'll always have conflict... All we can do is individually measure ourselves to be the best people we can possibly be, and part of that within my scope, is remaining eternally skeptical of any man or woman that proclaims at the top of their lungs that the voices in their head are divine... No matter how sincere their beliefs may be, or how good a person they may be in other aspects. Which, naturally, makes me enemies with fundamentalists.
tl;dr: We're social animals and we form packs by nature. Of course the various packs competing for territory and resources find reason to hate each other when their ideologies become irrevocably separate.