User blog comment:Morganamagic7/Agravaine and Arthur!!!/@comment-4532783-20111123005849/@comment-78.149.53.131-20111125231607

Morgana's mother was Igraine sister, meaning she was also Agravaine's sister. I think the reason he side's with Morgana is that she openly rebelled against Uther, who in his eyes was probably the reason for his sister's death, while Arthur stands by him.

It's also said that Morgana's mother was a Sorceress, so he probably grew up with magic, and does not see it as Arthur and Uther do.