Automatic alignments in games and other media bother me.

You're thinking from a modernist perspective where human cultures have extensively intermingled for thousands of years and we have very little competition with each other for resources.
If you look back even a couple hundred years ago our own world was similarly divided. Native americans were completely ensconced in their culture and to the invading christians that made them evil heathens.
In fantasy settings most races have not not had extensive contact with one another. They're all bound in their own cultural beliefs with the so called 'evil races' being defined by having traditions and beliefs in conflict with the so called good races. It's all perspective. Differing ideologies brook wars even today as Israel and Palestine show us weekly.

This is a good point, and those sort of situations are interesting. However, that's not what bothers me; what bothers me is when an entire race is evil--not just differing ideologies, not deep-rooted conflicts--just flat out evil and created and intended that way by the creator of that universe.