How can science replace prejudice?

Science creates facts and when there is a conflict between facts and prejudice, facts win. For instance, some primitive people led their followers to believe their gods would protect them from bullets. When they were confronted with a modern weapons they were killed. Science and fact won. Often prejudice persists because there is not a fatal conflict to eliminate it, and religious people most often run to the hospital to get help from science rather than rely on prayers, so they survive along with all their prejudices.