Yes they are different, the atomic structure is much harder to manipulate.
do me(and yourself) a favor... go find your physics teacher, and inform him(or her) that he/she sucks at his/her job.
all Atoms are fundamentally the same, they are created of Protons, Neutrons and Electrons.
now, what Magneto is capable of doing, is the he can remove the Electro-Magnetic bonds in the atoms.
the Electro-Magnetic bonds is what keeps the Electrons flying around the Protons instead of flying off.
so, the effect of Magneto doing something as Simple, as removing any electro-magnetic energy from Iron Mans armor, would be that every single electron in the atoms of his armor, goes flying. that means, that every single Atom in his armor would be instantly dissolved, leaving Tony Stark with no armor.
if he extends the field in which he removes the electro-magnetic energy, he would also instantly dissolve Tony Stark himself, not just his armor.
If he could do it on a regular basis, he would have. There are countless times that he could have used this power to his benefit, but he hasn't, and that shows that either A) It takes a large amount of energy to do it or He has some kind of personal vandetta against using it. We all know Magneto's hatred toward humans so B is out and that leaves A. In either case, If Magneto hasn't used it against bigger priorities than Iron Man, then he's probably not gonna use it against Iron Man.
no, it shows that C, the writers are aware that Magneto is extremely overpowered, and they are holding him back so that the comics are actually interesting and gives his opponents a fighting chance. kinda like they've done with Silver Surfer, Thanos, Nate Grey, Cable, etc. etc. etc.
and it shows that D, Magneto is not the hero of the comics and thus he never wins. it is for that purpose that sites like CBUB were created, to give a Realistic outcome of various fights, where people don't get held back for being overpowered, and where people don't automatically win or lose, simply because they are the hero or villain.
Magneto's powers: "Magneto possesses the power to control all forms of magnetism. He can shape and manipulate magnetic fields that exist naturally or artificially." - Marvel.com
"Although Magneto’s primary power is control over magnetism, he can also project or manipulate any form of energy that is part of the electromagnetic spectrum, including visible light, radio waves, ultraviolet light, gamma rays, and x-rays." - Marvel.com
this shows quite clearly that he easily has the Power to do it, now:
Magneto's Skills: "Magneto is a genius within various scientific fields. He is an expert on genetic engineering and mutation, with knowledge far beyond that of contemporary science."
"He has designed magnetically-powered aircraft and spacecraft, complex robots and computers, and magnetically-powered generators and created artificial living beings, space stations said to possess technology even Reed Richards would envy, and machines capable of nullifying mutant powers within a radius of several miles."
"Magneto has mastered many technological fields, and is an expert on genetic manipulation and engineering, with knowledge far beyond that of contemporary science."
this shows that he most definitely has the Knowledge and Skill to do it.
Bottom Line: since Iron Man is not staring in his own comic, and does not have the advantage of being the 'hero', and since Magneto is not being held back by writers needing to keep the comics interesting. Iron Man has no chance, whatsoever, and his armor gets removed from him in split seconds.