it is my educated belief that alot comes from the bible. the bible contains many, many isolationist and exclusive statements of superiority. we are god's chosen people, etc. the bible is full of judgement on the outsider, philistines, babylonians, etc. when judah and israel split, israel is the bastard.
so, yes, i think prejudice IS an integral part of the religion. but it shouldn't be. it is afterall a religion named after a man who said "love your neighbor"