I think what happened to Jake Lloyd is terrible, but it's essentially rooted in bullying. Children at school weren't making fun of Jake because the Star Wars Prequels ruined their childhoods (that would be quite a feat), they made fun of him because he was a child-celebrity. He was different. He stood out. Children will bully anyone who stands out. The Phantom Menace was a massive movie, so every kid at school knew that Jake was a celebrity, and even if that didn't cause his head to get shoved in a toilet, it unleashed a tidal wave of less-severe micro-bullying that can really beat a kid down eventually.
I don't think the Star Wars fans on the internet had much of any effect on Jake because he had no reason to interact with them (and honestly, they weren't that bad. The most I ever heard was "That little boy is a bad actor. That other little boy from The Sixth Sense is better"). AFAIK, his first "real" fan interactions were after he grew up and started visiting conventions, and a minority of attendees thought it would be appropriate to yell things at him or even stand in line so they can say terrible things to his face. But a minority of convention attendees are ignorant people who don't know anything about boundaries and think it's fun to sexually harass cosplayers. IMO, they're no different from childhood bullies. "Hey, I know that guy. Isn't he famous for being unpopular? Do you dare me to throw this half-finished drink at him?"
What happened to Jake Lloyd is really unfair, but I wouldn't put that on the people who hated the Star Wars Prequels. Plenty of Prequel haters have pointed out that it's not Jake's fault that he (as a child) was given a bad script and bad direction (which drew terrible performances out of some of the best actors in Hollywood). It was George Lucas who ruined people's childhoods, and that's not even remotely limited to the one movie Jake Lloyd appeared in (sand getting everywhere, Greedo shooting first, Kingdom of the Crystal Skull, the list is huge and Jake's single bad performance is only tangentially related to it).