Let's go back to The Incredible Hulk, one the bases for Marvel's Cinematic Universe. In the movie, the primary antagonist to Bruce Banner as well as the Hulk was NOT the Abomination. It was General Ross and the United States army. To this day, General Ross has been on a ruthless hunt for Hulk's blood, and nothing, not even his own daughter, has managed to stop him.
Let's fast forward to one of the most epic scenes in CBM history, where Tony Stark (a.k.a Iron Man) effortlessly walks into Hulk's movie to discuss a "team" they're forming. Cue the massive applause and endless chatter about the Avengers movie. To your average audience member this clearly means that Hulk will be teaming up with Iron Man, Thor, and Captain America. Well guess what? They're DEAD wrong. And so are you.
Frankly, it makes no sense for Iron Man to walk up to General Ross, the Hulk's most ruthless nemesis, and tell him that he wants to be an ally with his enemy. If anything, Tony Stark wants to ally with General Ross. But let's assume for a second that Hulk WAS joining the Avengers. That means that essentially Tony Stark said something like this:
Tony Stark: Hey General. What if I told you that we're putting a team together, and we want Hulk to be a member? Is it ok if we borrow him from you for a second? Oh, I understand that he's a convicted war criminal, as well as one of the biggest domestic threats this country has ever seen, and you have every authority in the world to hunt him down, but I firmly believe that he's a good person on the inside... So how about granting him a little amnesty. What do you say?
General Ross: %#$@ off!
Now granted, we never saw Ross's reaction. But I imagine it would be something like that if Tony Stark really wanted to be friends with the Hulk. It would also end with General Ross possibly detaining Tony Stark for conspiring to aid a convicted fugitive.
It is almost certain that the reason why Tony Stark was visiting General Ross was to discuss the fact that they both share a common enemy, and that this team they're forming is making him their number one target. In the comics, Hulk is a misunderstood creature who just wants to be left alone. Most people don't realize this and target him anyway. Tony Stark often finds himself at odds with the Hulk. (which is precisely why he built the Hulkbuster armor.) The heroes of the Marvel Universe have also skirmished with Hulk a countless number of times before. So it's not unusual for Hulk to be a bad guy in the movie.
If at first the Avengers wanted Hulk to be an ally, that would lead to some serious conflict between the Avengers, SHIELD, and the United States army. And yes, SHIELD is an enemy of the Hulk. Spoilers follow. Highlight them to read.
In the leaked Thor script, the Professor mentions a pioneer in gamma radiation, and how the second that SHIELD got involved, he never heard from him again. This makes it sound like SHIELD wanted to put Bruce Banner into custody.
Now, nothing doesn't say that later on in The Avengers, Iron Man and his team WILL find themselves at odds with SHIELD, and that Hulk WILL ally with the Avengers. As a matter of fact, that would be a VERY good way for the Avengers to split away from SHIELD and form their own independent team. It would also be a good way to create conflict with the team. Iron Man firmly believes in public safety over civil liberties. Captain America, on the other hand, is a staunch defender of just the opposite. This could lead to our first real taste of a Civil War movie....
Everything that we've seen so far points to Hulk being a villain in The Avengers. From the hints we've gotten from the cast members, to the rumors that we've heard, to the fact that we don't see Hulk anywhere on the promotional images. Hopefully, Hulk will not be the only villain in the movie. I'm dying to see Loki factor in as well. But I'm more than certain that Hulk is going to be a major threat to Captain America, Iron Man, and Thor come 2012 when they all join on the big screen together.