There’s a large number of books with the “man vs. the world” theme, and of the ones I know, the “man” has always been portrayed as right, even if he ultimately fails. (There are also plenty of film examples.) Have there been any where the “man” is ultimately proven wrong?
Go Ask Alice pops into my mind. She should have listened to all the squares!
Crime novels? Like Godfather, the Tom Ripley series, the Dexter series…
Isaac Asimov’s story “The Dead Past” comes to mind.
BTW, “man vs society” is actually one of the short story conflicts - novels usually are more complex than than (though films aren’t).
“I Am Legend” I think fits.
The hero is defending a society that doesn’t exist anymore and is actively killing the members of the new society. He is a monster.
“I am Legend”?
“I am Late in My Posting?”
Crime and Punishment?
Does “A Beautiful Mind” Count?
I dunno; I can think of several good examples of man vs. society novels. Any of the dystopian classics, for starters: 1984, Brave New World, Farenheit 451, etc. In fact, that particular conflict is probably better suited to a novel than a short story: “Society” is a very large and complex entity, and takes a lot of development (assuming that the society the protagonist is rebelling against isn’t our own, familiar one).
The Stars My Destination, maybe? Gully Foyle isn’t the most sympathetic protagonist.
Wouldn’t that be another one where “the man” was right?
I don’t know how similar the book and movie are, but “The Mosquito Coast” sort of fits (he isn’t directly fighting against society, though).
Camus’ ‘‘The Stranger’’? Suppose an argument could be made either way.
What about ‘‘Notes from Underground’’ by Dostoevsky?
Easy. 1984.
-FrL-
As BrainGlutton mentioned, Crime and Punishment is a good one. So is The Demolished Man by Bester.
Kafka said that “In the fight between you and the world, back the world,” but I can’t think of any of his novels where society is necessarily right.
Just about any book with an antihero protagonist might fit the OP. Or a villainous lead. Stephen King’s The Shining comes to mind. Or Ayn Rand’s Atlas Shrugged (Roark was a narcissistic asshole, after all). Or consider the collected X-Men comics… mutants are dangerous, after all! 
I came here to say 1984 too. Maybe “society is right” isn’t exactly how to put it, but definitely we’re shown how shallow and hypocritical Smith’s fantasies of being a defiant rebel hero were.
What, “he who wins is right”? Society wins in 1984, but that doesn’t mean Society was right. In any case it would be a case of “two wrongs don’t turn a pile of manure into a rose bush”.
He never figured society was right; he just knew how to place his bets. There are plenty of stories where society outlasts the protaganist, as mentioned by the OP, but not so many where society is the side you root for.
Some might consider “The Catcher in the Rye”, but that’s a fairly mixed message - another case where neither side is necessarily shown to be right.