Tony Stark is not a villain, but he could be. After all, he is a genius. He made revolutionary weapons before giving it up, and anymore, nearly everyone uses StarkTech in some capacity. He could totally take over the world.
Of course, no one realizes just how close he's come to being a villain.
Sometimes, he wants to be one. After all, the villains don't have to go to debriefs after long battles where they're forced to justify their actions. And people may hate villains, but it's expected.
You don't expect people to start demanding retribution for the method used to save the freaking world (but it happens).
A villain doesn't have to trust anyone, because betrayal is expected. You don't expect the hero's father-figure to try and kill him, or his best friend to steal from him (but it happens).
But, Tony Stark is not a villain because, at the end of the day, that thieving best friend will fight for you, there's dinner with the team after a debrief, and, most importantly of all, the hero's the one that gets the girl.