If your high school coach is anything like my son's I wouldn't worry about it hurting his chances. If he is on one of the top travel teams in the country,chances are he should be getting noticed by college coaches following the travel team. I don't think a lot of college coaches put much stock into what a high school coach thinks anyway. They see the bad ones for what they are,guy's just out to collect the extra $3000 per year to coach the team. If your son is that good, then the decision not to play him is more a reflection on the stupidity of the coach and his bias toward your son.
My son has been receiving college offers from coaches who have seen him play during his travel season, not during his high school season. Good Luck !!