"if it turned out we were in a simulation, that would almost by definition mean that our universe was intelligently designed (even if the design were merely a one-for-one replica of a non-designed universe). I think that such a scenario is unnerving to many people because it would introduce the possibility that the designer(s) might be able to express agency in the universe, and towards humans individually, in a way that the cold unfeeling laws of physics do not."
Excellent point - one I hadn't considered too deeply. I would also imagine it would challenge the ideas of religious people around the world. "Mine is the one true faith. Therefore my God(s) created the simulation" sort of thing. It would probably bring about completely new religions come to think of it.
Let's hope its not a simulation.