the ideological conflict between Captain America and Iron Man was always designed to have a "correct" side—and it isn't the one the fans chose—according to a Marvel writer on the project, which led to the Civil War event in 2006, which transformed the Marvel Universe for all time. The argument between Steve Rogers and Tony Stark led to a worldwide conflict involving almost every superhero in existence and sadly resulted in Rogers' death. Iron Man was always the true protagonist of the tale, according to Marvel writer Mark Millar, so the conclusion wasn't particularly bittersweet.
The villain Nitro detonated during a skirmish between the New Warriors and a gang of bad guys, sadly killing hundreds of bystanders. As a result, the US government promoted the Superhero Registration Act (referred to as the Sokovia Accords in the MCU): a set of regulations defining exactly how superheroes may function in the nation. All superheroes had to register with the government, go through required training, and divulge their true names to the authorities, among other requirements. These restrictions were upheld by Iron Man, but Captain America rejected them, causing a divide that ultimately resulted in the Civil War.
The readership was as divided as the heroes; while some saw the Superhuman Registration Act as a necessary response, others saw it as blatant overreach on the part of the government. Both characters occasionally behaved in ways that were inconsistent with who they were, which confused and angered some Marvel fans. In an interview with Gamesradar.com, Civil War author Mark Millar clarified his side of the story, saying that Iron Man was always intended to hold the moral high ground:
"Strangely, several of the other writers frequently portrayed Tony as the villain, which I found odd considering that I supported Tony. In the actual world, if someone possessed superhuman abilities, I'd like to see them registered in the same manner that a gun owner must have a licence. However, a rifle can kill several people but a superhero can murder thousands, therefore from a practical standpoint I completely support Tony. Cap's position may make sense romantically, but I don't believe anyone would actually desire that in the real world."
Was Iron Man always correct?
The bulk of Marvel fans disagree with Millar's remarks, believing that the superhero community should maintain its autonomy and Captain America's point of view. Although Millar's position favours pragmatism over enlightened idealism, the argument that those born with superhuman talents aren't always born with the ability to control those skills is valid. The fact that Captain America passed away at the conclusion of the event definitely seemed to support Iron Man's (and Millar's) argument that independent-minded superheroes are inherently dangerous and will eventually cause tragedy.
Keep in mind that Millar is only discussing the comic book adaptation of the story (Civil War is quite different in the MCU and has nothing to do with secret identities, merely government control over super-powered individuals). Even yet, other writers on the project didn't understand that Civil War was meant to have a "right" and "wrong" point of view since they disagreed on which superhero was more morally upright. Civil War remained a key topic in discussions about superheroes, morality, and whose character had the moral upper hand: Captain America or Iron Man, more than fifteen years after the event was published.