Personally, I think the evil of religion stems from the systems of morality presented by religion. Each one has its own set of rules, but any set of rules which cannot be summed with "improve the wellbeing of other people" is immoral.

Morality means being kind to others, but religion tricks people into believing that whatever their religion asks them to do is moral. So when a controversial situation appears, instead of looking for the option which best helps people, they look for the option which agrees with their religion. That is the root of religious evil.