No, it is definitely not Pettigrew, it is Snape. The "many masks" refer to the many layers of personality that he wears (spying for the Order, he wears a "mask" of loyalty to V; he's a kiss-up to Malfoy, but at all other times he's highly independent, and so on), as well as a Death Eater's mask.
The intended breakdown of the riddle is like this:
Masks I wear many,
But not many see behind them. (DE mask, plus the "masks" of personality he wears as a spy)
Except by those dark as the one I despise. (all through the books he sort of hangs on the outskirts, and sometimes is even openly snubbed - except by Voldemort, to whom he's apparently a great asset, and by the other Death Eaters, who recognise him as being powerful and respected by V.)
I hate and I fear One of whom I will not speak
Yet I throw myself continually at his feet. (Snape refuses to use V's name, but he has to keep "serving" him in order to spy for the Order.)
I am continual. (This was just bad writing on my part.)
When all other hope is gone, I remain. (OotP: when Dumbledore is on the run, McGonagall in St Mungo's, Sirius "kidnapped," and the Floo is being watched, Harry's only hope of contacting the Order is to send a message in code through Snape ("He's got Padfoot! He's got Padfoot at the place where it's hidden!") in the hope of saving Sirius from V at the DoM.)
Those I defend I do not love, (there's certainly no love lost between Snape and his students; whether or not he "loves" DD in any way is still a subject of debate)
And those I fight I cannot hate. (He can't actually hate the DE's, because he was once one of them; so no matter how much he detests their actions, he sort of knows where they're coming from, too.)
The one who hates me most (Harry)
Is the one I will die to protect. (Some people have disputed the "will die" in this line, but it wasn't intended as a prediction. It was something more along the line of an oath, that he probably promised at some point to defend Harry, even if it means dying himself. Although he's never actually been put in a life-threatening situation in order to help Harry, I could go through the books and pick out at least 4 instances that I'm aware of where he does go to some kind of risk in order to help Harry.)
It was a nice try, but it was deliberately written to point to Snape. You did support your theory fairly well, but there are still too many loopholes - who would Pettigrew be dying to protect, for example? And why is he the last hope . . . okay, I guess I could see where you could say that he was V's last hope for regeneration, scratch that.
Boy do I feel lucky I have that line in there about dying to protect someone, you could probably trample me otherwise ^_^
Okay, somebody else's turn . . . maybe I will have to write another one and then send all my friends here to revive it . . . hmm . . .