Many evolutionary psychologists would say that at least part of it does have roots in natural selection, but not in the sense that prejudice itself is a carefully designed adaptation.
A common argument goes like this:
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For most of human history, people lived in small groups competing with other groups for territory, food, mates, and security.
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Individuals who were highly attentive to "us" versus "them" may have survived better.
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The human mind therefore evolved tendencies toward tribalism, conformity, suspicion of outsiders, and loyalty to one's group.
That does not mean hostility toward immigrants, racial minorities, gay people, or religious minorities is genetically programmed. Rather, the underlying tendency is to divide the world into in-groups and out-groups. Which groups get placed into those categories is heavily shaped by culture and circumstance.
One clue is how variable the targets are. In one era people fear Catholics, in another Jews, in another immigrants, in another homosexuals, in another people speaking the wrong language. The specific target changes, but the psychological mechanism—group identity and perceived threat—looks similar.
Your observation that it often seems irrational is shared by many historians and social scientists. Much prejudice persists even when:
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the disliked group poses no realistic threat,
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cooperation would benefit everyone,
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the facts contradict the fears.
Humans are not purely rational creatures. We are very good at constructing reasons for feelings and loyalties that arose for other causes.
There is also another force besides tribalism: status competition. Sometimes opposition to civil rights is not driven primarily by hatred but by fear of losing relative position. If one group has historically enjoyed advantages, equal treatment for others can feel like a loss even when no actual rights are taken away. That perception can be politically powerful.
The interesting thing is that humans evolved capacities pulling in the opposite direction as well:
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empathy,
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cooperation with strangers,
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moral reasoning,
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universal principles.
Those capacities allowed ideas such as religious tolerance, democracy, civil rights, women's rights, and gay rights to emerge. From a purely evolutionary perspective, humans are unusual because we can consciously decide that a principle should apply even when our instincts might favor only our own group.
So if you find yourself thinking, "Human rights should apply to everyone, otherwise they aren't really human rights," you're following a line of reasoning that appeals to universal principles rather than tribal boundaries. Many philosophers would argue that this is one of civilization's major achievements: extending moral concern beyond the small group for which our ancestors originally evolved.
The tension between those two tendencies—tribal loyalty and universal morality—runs through much of human history. Civil rights movements, including those for racial equality and gay rights, can be viewed as efforts to persuade people to let the second tendency override the first.
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