If Peter Parker isn't a loser, he's not Peter Parker (or at least, not the Peter Parker they're adapting - those early 60s comics). People aren't mean to Peter because he's actually great and brilliant and misunderstood and they're just cruel awful people. They're mean to him because he's a weirdo.
That's why Hollywood so often fails at portraying "nerds." They're usually just good, handsome, charismatic people with some glasses slapped on them.
Real people get bullied for a reason. Tobey makes weird faces, he pauses and stares, he says stupid shit all the time. He has no spine at all. He takes the abuse and shrugs because it's his lot in life. He has a good heart, but it's compromised by selfishness and fear. That's real. That's my life up there on the screen. That's why it works.
In Spider-Man 2, when he knows MJ has a boyfriend, he starts hanging around and reciting poetry despite thinking that's gonna somehow win her heart? God, I can barely even watch it because I remember being that guy.
I mean, sure, he's like 30 years old and pretending to be a high schooler but...