From what I could tell it was popcorn that was "thrown" at him. Not that it makes it less of a classless thing to do, but it's not like there were meals being tossed around. Granted, this is purely from what I could see on the cart in videos of him being carted into the locker room, and I wasn't there, so I'm not going to claim this to be 100% factual. Here's the video where I could catch a glimpse of this:
http://www.nfl.com/videos/san-francisco ... an-injured
If you don't want to see replays of the knee then skip to about the 1:03 mark. There's a handful of popcorn kernels on the cart. Likely the work of just one rotten apple.
That being said, it was a horrific injury and I do wish him a speedy and full recovery. Hate to see those injuries happen to anyone, especially such a gifted young player like Bowman.