In short, and very quickly: because it is a terrorist act.
Terrorism is violent acts done to intimidate people, particularly an identifiable group of people, into submission to a political entity. Al Qaeda is political: they want Westerners out of their countries. (We'll leave aside the argument that they are turning every country into "their" country.) The IRA was political. The Palestinians are political. And this Terry Jones is political. He's not doing this for God: he's doing this to protest the community center near Ground Zero. He's doing this to intimidate Muslims. He's doing this to spread fear.
He's using violence to deprive Muslims of their equal enjoyment of American freedoms. That is terrorism.