Well, a lot of reasons, really. Some of them relate directly to the movie and others to the culture of film and film reviews in Hollywood. Some are legitimate and some arbitrary.
Although none of them will be fixed by fans ranting on the Internet that "It made more money than all ten of the Best Picture candidates combined! All of you will burn in hell for this!".
None of this is to say that The Avengers doesn't deserve all the accolades it got, and probably some awards, but to contextualize things so that every time somebody "snubs" it people don't wonder what just happened.
It's just not that kind of movie.
And, frankly, nobody much ever thought it was. The whole idea that The Avengers is being slighted by a lack of awards consideration is really a creation of the fans, something that springs from affection for the film and causes you to reject the notion that it's not "the best."
But there are different metrics for measuring "the best" and technical excellence in filmmaking is really the standard critics and awards nominating boards are meant to be considering. From that point of view, they're looking for something entirely different than what Whedon and company set out to do. They set out to make a movie with the broadest possible base of potential fans--one that appeals to everyone.
French fries appeal to almost everybody, after all, but very few people will admit they're objectively better cooking than good sushi, which appeals to a much smaller number of people.
There's always a struggle between art and commerce, and most movies are made with commerce in mind. It's rare that those movies get awards love, and it's often because the people voting think that they've already got what they wanted and deserved--the popularity of their film and the money that goes with that.
Little filmmaking choices sometimes make a big difference, too; the choice to do a lot of the effects as CG rather than practical effects gave the film a decidedly different look than either The Amazing Spider-Man or The Dark Knight Rises, both of which used practical effects as much as possible and both of which are more likely to be considered for a number of technical awards as a result. The SAG nominations for those films' stunt units bears this out a bit.
It's also a sequel, but not a finale. It tends to be that few such movies get the credit they deserve, with voters thinking they can always give the last movie in the series an award for overall achievement.
There wasn't a stand-out performance.
The Avengers was a true ensemble movie. Almost everyone in it was good, but the only character that really stole the show was The Hulk, and most of that was post-transformation, meaning that it had as much to do with the effects people (who will almost certainly win a raft of awards this year) as actor Mark Ruffalo.
And before anyone says it--yes, Hiddleston was great. And yes, he's the kind of actor who wins awards. This is also his second turn as Loki and he didn't do anything appreciably different this time from what he did last time, when he wasn't considered for awards either.
Most of the time, when a big "popcorn" movie gets a lot of awards consideration, it's because there was one particular actor that just blew everyone away (often the villain, which can give the film a Hannibal Lecter complex). That's what happened with Ledger as The Dark Knight's Joker, and you can go back farther than that to find dozens of similar examples.
There was also no clear lead actor, meaning that the idea of a Best Actor or Best Actress nomination is pretty much out right away. Then, even assuming there was a strong enough stand-out performance to rate a nomination, they would be competing (at least potentially) against all of their co-stars for a Supporting Actor nod.
While the twin successes of The Avengers and Much Ado About Nothing might change this, as it stands the Cult of Joss is mostly made up of fans, with critics a bit dubious. In the film community, he may be popular but a guy who works on big budget blockbusters and TV series doesn't fit the mold of the most revered filmmakers in town.
Iron Man series directors Jon Favreau and Shane Black actually mix better with the awards show crowd, having paid their dues on indie films before breaking into the big-money stuff with crowd pleasers.
And it's for those reasons and others that this one is the weakest reason--those walls are coming down all the time, with guys like David Fincher working on The Girl With the Dragon Tattoo, Christopher Nolan on Batman and Sam Mendes on James Bond. The idea that a guy like Whedon is going to be Marissa Tomei, an embarrassment to the establishment should he turn out to be the winner, is a mentality that's on its way out.