I also remember that he specifically said he wrote him that way because of 9/11.

He saw Magneto not just as a bad guy but specifically a "superior race" leader of a terrorist group. Morrison acknowledged that Claremont's work to give him a motivation that justifies his position was great writing, but then 9/11 happened and he suddenly couldn't see any violence done in the name of ideology to be anything other than madness and idiocy no matter the justification, so he decided to write Magneto as a mad idiot.