Yeah, booing Ruffalo was rude. As much as I wanted Ed Norton to be Banner, I hold no animosity toward the actor replacing him. In fact, I would think him crazy to not take the role. Now booing Kevin Feige? Well, still rude, but at least it would be directed in the right direction.
What did people think would happen? That he would get clapping? Ruffalo probably shouldn't have even gone to Comic-Con, since many fanboys are still pissed about Norton being kicked off.