It is easy enough to make a case for Artemis Fowl being evil. He's trying to steal, kidnap, break an ancient society. He's a criminal mastermind, for gosh sakes. That's easy enough.

However, the fairies and other magical characters don't act in such a way as to convince readers they are truly good. You could justify their actions, via self-protection, political necessity, and/or tradition, but not through pure ethics.