I'm not saying it makes sense, but Islamic protest of media is fairly often and insane.
However, I agree that the video probably isn't what actually caused the embassy attack, but I'm not sure it matters now. Now that the theocratic Islamic culture is aware of it, that's all that matters. It will be their rallying point.
I find it frustrating that free speech is a concept so unacceptable to that kind of culture, but I get it. For them there's no reason such a video should exist. If it happened here and our government didn't stop it, our entire country is responsible. It's the result of minds conditioned to living under theocratic rule. There isn't much that's more dangerous, IMO.
And this is why I always side with civil liberties.