My grandmother told me she used to go to the department store and they had separate bathrooms for whites?

and non-whites and she was a young girl and didn't know why and her parents told her to be nice to everyone but that blacks and whites didn't ociate with one another. Both her and my grandparents went to church, this was in the south. This makes me sad b/c in the Bible there was a mixed multitude that came out of egypt so I don't know why so many christians were okay with this. Please explain, thank you