After his escape from their clutches, Stark quickly develops a hatred of war profiteering and the military-industrial complex (which, if the movie is to be believed, his company leads). This might make things a little more clear, except that he continues to delight in building outlandish weaponry and deploying it against the sneering Afghan baddies. Only in Hollywood can you charge millions of people ten bucks to gape for hours at extravagant gee-whiz weaponry while simultaneously decrying capitalism and U.S. militarism.
Hollywood has been trying to make money at their political opinions for a while now through the release of a myriad of anti-war films, the bulk of which have failed miserably at the box office. Perhaps Iron Man could be the exception?