Perhaps in some cases because Kevin Smith doesn't like it, fans of Mr. Smith will not bring themselves to like that movie. They don't do it on purpose, but subconsciously. They rent the movie in some cases wanting to hate it.
As for commoners disliking the film, these are the people who go and buy Big Macs at McDonalds everyday (McDonalds, there's a horrible store.. At least at Burger King they let you choose what you want on it, at McDonalds they premake all their burgers in the morning and freeze them, nothing is ever fresh, it's disgusting). They don't like films told in a unique or different fashion, and they don't like out of the ordinary. How can I make such a broad generalization about people? It's easy, just look at McDonalds' sign."Over 99 billion foods sold per day" (took some poetic license there). I'm not saying that all people who like McDonalds hate Magnolia, don't get me wrong, I'm saying that all people who hate Magnolia eat at McDonalds.