For multiple reasons, really.
In general I think the biggest one is because it's so far off from what you'd expect Disney to do. Its like if Mel Brooks was asked to produce a Disney movie.
Back then, this was the first Disney film is years that was not a blockbuster musical romance with a "be yourself" message. It was pretty radical for Disney actually, especially considering that this actually came out before Shrek.
And I think it's also because this was a movie that wasn't even really supposed to exist. So much shit happened during production, so much of it was changed, that instead of doing a generic fantasy tale, they just threw their hands in the air, said fuck it, and made a completely different movie that, instead of trying to be a dramatic and epic, it was funny, short and completely different from what Disney was associated with.
They stopped giving a shit and just tried to be as funny as possible while taking a piss on the Disney cliches they were supposed to incorporate into the movie.