I think there is some confusing verbage in the opening post but I think I get it... for example... "plays great but doesn't get in the lineup". I believe OP is saying they put him in defensively but not in the hitting lineup (sometimes, summer ball is run loosely to where this is not uncommon).
BJE, first, welcome to the site. I think I can relate to much of what you and son (and coach) are going through. I do have some of the same questions as others, particularly regarding how much of this you are relying on your son telling you and how much you have actually heard/observed first hand.
I am a HS coach and we just finished our summer program. It is much as you described (games, no practices, developmental). Also, many of our key players are off playing more competitive travel ball somewhere. And, being summer, having a steady roster is non-existent. Sometimes, we have to pull up guys who are not ready to play against V competition yet. Sometimes the opponent is full of V players and sometimes not. We had a very similar situation with our catching position, where there is a significant drop in talent level between the usual V catcher(s) and who we often had with us for summer. They had a very difficult time keeping runners from taking bases at will and sometimes had difficulty handling better pitchers than they were used to. It can be a glaring weak spot and really effect the quality of the games. That said, it is no fault of the young player being put in that position. Still, frustrating for all involved. Sounds like this coach may not have handled it well at all but take into consideration that some of this may be interpretation/ what your son is hearing vs not hearing. Without being there, I have no idea what the coach' motivation is for handling it this way but he may just be very frustrated. This, too, is common... just finished regular season with varsity players and now coaching games against some of the same teams with several players who are definitely not varsity players.
I don't know that he is crossing the line or doing anything that would be worthy of talking to the HC. I suppose it depends somewhat on what, if anything, was promised with regards to the summer program. Most of the freshmen (even a few incoming freshmen) consider it an honor and great opportunity, even if they get minimal PT. We make a strong effort to get every kid some defensive innings and some AB's in each game. Some programs still bring 15 - 20 kids and many don't see the field. I suspect that your son is very aware of where his shortcomings are. I would just turn all focus toward getting better and coming back and proving himself to all the coaches that he can be a player that will help them going forward.
It is not uncommon for players to get called out by their coaches. On the surface, it sure seems like poor tactics or poor character by this particular coach in this particular scenario but a player must be able to handle being called out directly and turn it into fuel instead of letting it stand in the way of his goals.