Pretty sure it is the grades. My son attends a JUCO, and he has a friend on the team, who my wife and I love. However, the coaches apparently aren't real happy with him. It was really hard for me to understand why. His dad is a local HS Coach, who was a closer at a major D-1, and this kid is a great athlete. He's respectful, and a real joy to be around. With all that being said, I asked Ryno why the coaches didn't seem to like him. Ryno said they think he is "lazy". I said why do they think that? He said, "because of his grades. They don't think that he works hard enough to take care of that end of the bargain." He also said that he only wants to stay in his room and play video games all the time.
I am pretty confident it is the grades. Ryno is a very bright kid, but I keep on him about his grades EVERY time that I talk to him. Last semester was his first, and he had a hard time with a 200 Level Business Stats Class. (Not sure why they would suggest he take that in his first semester of college.) I told him constantly to get with the professor to find out what he can do for extra credit, additional classroom time, get with a student who understands the material better, etc. It ultimately didn't lead to him getting an A in the class, but I know that he did his part to try and make it happen. He ended up with a 3.6, and his lowest grade this semester is a 95%. My point is that I am constantly discussing this with him because of the importance to his future. If he transfers to another college, it lets those coaches feel confident that he can handle the load without them having to baby sit him.
I would talk to your son and find out what classes he is struggling in. Then I would advise him to meet with each professor and develop a plan of attack to get his grades up to a MORE than satisfactory level. Then, I would have him talk to the coach and apologize for his "laziness" in the classroom. I would also have him tell him that he is sorry that the he has provided undue stress to the coach because he didn't take care of his business. After all of that, I would have him stress to the coach that he is going to make changes, and he will get his grades where they need to be. Then, I would have him ask to PLEASE give me another chance.
If that doesn't get things on the right path, then I would consider looking into the transfer idea, or give up baseball all together to get my academics right.