If you've read his Authority, you'd know just how conservative Millar is. If Iron Man's side was the good guys, Hill wouldn't have attacked Captain America illegally, wouldn't have come down on Patriot like the Fist of God, Stark wouldn't have created a cyborg clone (without Thor's consent) that killed Goliath, wouldn't have thrown heroes into the Negative Zone, wouldn't have attacked Spider-Man and sure as hell wouldn't have recruited villains like Venom, Bullseye and Deathstrike.
The writers insisted that there were no right or wrong sides, even when Reed argued in favor of government witch hunts. They were far from fair and balanced ;)