This happened at the Wylie vs. Horn game last night, and I was curious about the exact call. As was everyone around me. (And I sit with the "Football Intellectuals" 
The snap was high and went over the punters head. He picked it up, and ran a bit to the outside. At this point, he was well outside the "Tackles" and about 20 yards behind the line of scrimmage. When the kicker kicked it, the Wylie defender was in the process of diving to block it. He ran into the kicker, and the ref threw a flag and called it "running into the kicker"... I thought (for some reason) that if it was a botched snap and the ball hit the ground, he was no longer considered a "punter" and became fair game. The ball was well off when he was hit, but should the call have not been "Late hit" and not "Running into the kicker"???
Also, would a late hit not result in a first down, whereas running into the kicker or quarterback is an automatic first down? It's late and I'm tired, and may not be explaining this correctly.
The kicker does not automatically lose protection because of the botched snap. I thnk that may be a rule in the NFL however. In our game (NCAA rules are used in Texas HS), the kicker can "re-establish himself" by setting himself and making it obvious he intends to kick. If he can do that , even under heaby rush, he gets the protection. If he is runing for his life and just kicks it while on the run, he is not going to get roughing the kicker protection.
Late hit vs roughing the kicker : Late hit means the hit was after the ball became dead so that likely does not apply here. There is a foul if you hit someone who is obviously out of the play but that is not called a late hit. Late hit and roughing the kicker are personal fouls. Both carry automatic 1st downs as a penalty. However, if the late hit happens after 4th down and the offense had not made 1st down yardage during that down, then they will not get a 1st down. The ball would go over to the defense and defense would start 15 yards further back than they should have.
