[Crazy Jetty]

Agreed with Megaprime. Doom knows his own weaknesses in any given situation, and he knows the armor he wears would be his greatest weakness against someone like Magneto, so he'd have plans to protect himself.
Beyond that, he's also Marvel's second greatest sorcerer, yes? Second only to Dr Strange, right? He's also way smarter than Magneto, as well (This is not to say I think Magneto is an idiot. But it's true, Doom is one of the most intellegent characters in Marvel or DC).

Either way, it's a good question, because if fate ever worked out for either of them, the two would eventually cross swords. Doom has no interests in mutant affairs, and he would either have to prove to magneto that his new world would allow mutants to florish in peace and prosperity, free from persecution and prejudice, or just take him out.
I think Doom would do the later. It's simpler.

Likewise, if Magneto was ever able to bring about his new world order with mutants as the dominant lifeform, Doom wouldn't just roll over and allow it.

I don't think Magneto can defeat Doom one on one.