I think he was probably more upset with the amount of time it took to throw the flag rather than the flag itself. It took like 2 minutes after the play before the flag was thrown, and to that end, I can't blame him for being upset. I'm sure he'll watch the replay and understand why it was thrown because it was so horribly blatant. That kid who made that hit should be disiplined.
I had some buddies at the game and they said the official threw the flag right away! They the officials got together and talked about it, before he called the penalty. So the ref threw the flag right away, but they discussed it first, as any good crew should do.