The one thing I know is when my brother, husband, and nephews all played/play football, I had to always sit where I couldn't see the coach for this very reason. The sport is VERY amped and the coaches seem to scream, yell and carry on all the time and it drives me crazy. My brother told me just recently actually that this is part of football and that's why it's not for everyone. You just have to toughen up and suck it up.
Now that being said, it sounds like your son's coach was way out of line but it doesn't sound like it happens often. He may have just made a mistake or maybe he saw something in your son that he wanted to improve and it had nothing to do with how he was doing his job. My husband actually said that coaching the really good players is harder because you want to ride them all the time to make them better.
You didn't mention how this made your son feel or if he wants you to talk to the coach? To tell you the truth as a good JV freshman player, I think your son needs to be the one to talk to the coach about it, not mommy and daddy. He is perfectly old enough and mature enough to get to the bottom of this situation. From your post, it sounds like a one time thing, but if your son is actually being bullied from this coach then that would be different and you need to step in.
One last thing to remember is, he has one game left, and then next year to look forward too. If he is that good, he probably will move to Varsity anyways and not have to deal with the guy again.
Truly it sounds like this guy was just out of line in this instance, people make mistakes. I would let it go.