Might it be at least somewhat lower level than that? I'm thinking along "selfish gene" lines. You are more likely to share genes with people that look like you than with people that look nothing like you, and so favoring those who look like you should help copies of your genes to make it into the next generation. A genetic predisposition against people who look too different could be selected for.
There is plenty of literature on this idea:
Racism is the modern manifestation of very primal instincts and behaviors which are an integral part of human groups and societies.
To work well as a society, you need to have an identity, a sense of self, of cohesion. For that, you need some contrast, an opposite. Other religions, other countries, other skin colors. They all provide a convenient object for differentiation.
In addition, it wasn't long ago that hunting, aggression, violence was an essential part of survival, and we all still have those instincts. This aggression is mostly under wraps and deeply hidden in modern society, but it's present. And it needs to be directed somewhere, outside of the group.
The more presence a different group gets within your own, the more differentiation and multitude of variety, the more prevalent racism becomes. So the more international and diverse we become, the bigger the problems with racism.
And with smaller satisfaction/happiness, there is more aggression.
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Sadly, I really don't see a solution in the short term. Our brains are just not wired for the happy, inclusive, diverse, all accepting wonderland lefties aspire to.