Marvel's Magneto is among the most famous of X-Men villains for a very simple reason: unlike many comic book enemies, the Master of Magnetism has heroic intentions behind his actions. Magneto can occasionally be selfish, cruel or vindictive, but his overall goal - to protect mutantkind from the homo-sapien hatred - is a noble one. In New Avengers #6, even Iron Man agrees with his ends, if not necessarily his means.
Magneto appeared alongside the X-Men in Uncanny X-Men #1 as the team's first-ever supervillain. Back then, Magneto was a far cry from the complicated, multilayered antihero found in the Marvel Universe today; he was a simple mutant supremacist who believed mutants, as homo-superior, should inherit the earth from homo-sapiens. When Chris Claremont took over the series, he memorably made Magneto a survivor of the Holocaust in Uncanny X-Men #150, released in 1981. From that moment on, Magneto has been inextricably linked with persecution and the freedom of all mutants from the tyranny of oppression.
In New Avengers #6, a feature appears after the main story: Avengers Assemble: The Oral History of the Earth's Mightiest Heroes. The Avengers sit around a table and reminisce about their past; they remember Edwin Jarvis, Tony Stark's butler; they discuss fighting the Greek God Zeus; they talk about going up against Magneto, old enough to remember World War II's atrocities. Regarding Max Eisenhardt's worldview, Iron Man mentions "...this is going to seem odd to say, but he wasn't wrong...even though I don't like him on any level and absolutely, with every fibre of my being, despise everything he has done in the name of his cause...I do understand it. He isn't a criminal in the truest sense of the word."
Iron Man and Magneto have fought before, and while Magneto certainly has developed as a character since the Silver Age, the same can be said of Tony Stark. Before his kidnapping in Vietnam (later retconned to Afghanistan), Stark was a hedonistic weapons manufacturer who held little regard for anyone other than himself and cared little for whoever his weapons hurt. This black-and-white mentality was shaken once Tony devotes himself to changing as a person. If he is worthy of a second glance, so too are his enemies, including Magneto. The Tony Stark of the past wouldn't even dream of regarding Magneto as a person with noble qualities, but Stark of the present is willing to see a person's true intentions.
Magneto has committed evil acts but that does not make him an evil person; he sees his means, however violent, as the only way to protect the mutant race from another Holocaust-like horror. Some heroes like the Punisher are 100% uncompromising in their views. But Iron Man knows that there exists a world of grey that most people are unable to see, and Magneto is a prime example.