Can someone please help me find the rule on roughing the kicker? We had a situation in our game where the snap to the punter was bad and rolled back to the punter, after finally picking it up the punter got the punt off just before being hit. Am I wrong or is the punter considered a running back if the snap is muffed or hits the ground?

Only in the NFL does he get no protection just cuz the snap hits the ground. In NF as long as "it is reasonably certain that a kick will be made" (9-4-5) he is awarded protection. Now you need to give the defense some slack if he picks it up and all of a sudden kicks it. I'd have to see it, but if the defense was not sure he was going to kick it, then I would not have roughing.

You're wrong.

Whether the ball hits the ground or not, a kicker is entitled to protection.

You would have running or roughing if the punter made no running back moves. However if after the recovery of the bad snap the punter starts to run...then kick I believe rule 9-4-5a: "contact is unavoidable because it is not reasonably certain that a kick will be made".

I tried to have an "observers" discussion with my fill-in referee just a few weeks ago on this very subject. Since I was unable to do the game (bad ankle) I timed from the booth and watched a bad snap fielded fairly cleanly by the punter and he got the kick away without moving more than two feet. Meanwhile, he gets leveled by the rusher and there was no flag.

I told him what I saw and he insisted that once the ball hits the ground the protection was off. He just wouldn't listen to me. What made things worse he turned his attention to the flight of the ball which of course he denied he did. It was at that time the kicker was knocked down.
It was pointless to continue the discussion, the fact of the matter is, protection is not automatically removed just because the snap hit the ground.

Again, it doesn't have to be a bad snap. He could just take off and start running. He may pull up and actually kick the ball. Now the officials judgement (with 9-4-5-a in his hip pocket) may come into play. The defender still does not get a free shot at the punter.