For the same reason why people do that in every country to each other. Religion, incompatible cultural values, ideologies that go against other people, ... It's sadly something people do and have done everywhere in some way or another.

In Transjordan and the greater area between Northern Africa and Asia there were countless shifts and movements, mixing and separation of groups for all kind of reasons. But I think the separation because of different religions is probably the reason that lead to the biggest rifts, at least in that place.

I don't see how that has anything to do with whether or not a group of people is native to or had ancestry in a land.