(I’ll play devil’s advocate here because obviously I don’t [edit: missed word] condone any kind of prejudice or racism. So please take what I am about to say not as something I endorse.)

Religious intolerance at least makes more sense than racism based on nationality. You cannot choose what nationality you were born into. And while religion is not always a choice, it can be changed. This is why we had crusades, why people convert, etc. I cannot make a white German an African American, but I can convert a muslim to christianity.

This also matters much more than nationality. Religion or faith in general is based on rules about how to live your life. And as much as you want to be living independently - you cannot live by your set of rules if everyone around you has a vastly different set of rules. The rational response would be to find a compromise and adapt. The subconscious response often is “change your rules to mine”. Because rules can be changed indeed. Skin color can’t.