Some coaches are very cautious about their recommendations. Top D1 programs will ask if a player is the best player on the team and in the league and they are serious. Go look at the bios of the kids from a nationally ranked D1 program and you will see that almost every player was all-league, all-city, all-state, etc.
Of course at a lower tier D1, a D2 or a D3 they aren't getting that caliber of player.
In the end, brod is right that although the HS coach can help the most important thing is for the college coach to see the player.
HS coaches typically have pretty low opinions about the baseball acumen of parents, no matter their baseball backgrounds, if you haven't noticed. Well the reality is, justified or not, college coaches feel the same way about many, though not all, HS coaches so don't be too worried about the coach's recommendation as long as he isn't being negative about your son's character.