It's not a new concept. Throughout history people have hated (or feared) those who are different to themselves. It's ill-educated, because if you take the time to get to know somebody, anybody, you'll find there are far more similarities than differences.
So how am I going to tie this into writing? Well, I'm thinking about how all good drama is based on conflict. Xenophobia can be the basis for multi-layered conflict. A character has all the external conflict of dealing with the object of his mistrust, possibly coping with people trying to convince him he's wrong, and the inner conflict of reconciling long-held beliefs with a changing reality. It doesn't even have to be a major prejudice, like hating black people, or Muslims. You can have your character hate cheerleaders in an irrational, xenophobic way. The conflict will still be there.
Do you have any xenophobic characters in your work? How do you utilize them?