It has to start with the coach if a program has great chemistry year in and year out. Players come and go, but the constant is the coach. (assuming he is there for awhile)
Quality coaches build strong rapport with their players, which in turn develops Sr leaders, who then build up the under clansmen and so on. We're not talking fully funded P5 programs, you will find great chemistry programs throughout the college baseball spectrum, from mid level D1's to low level D3's.
Prospective recruits need to look for this during practices during visits, and parents can get some indication by meeting with the coach. In the end part of our decision was whether we were comfortable having our son play for a man for four years and 2,500 miles away. He was a class act and developed great young men who in turn built a program with outstanding chemistry, which in turn developed into one of the top programs in their division. It happens year in and year out because of the coach.
This is a good subject and should be helpful to players and parents going through the recruiting process. Tight highly motivated teams don't just come from high visibility highly funded programs IMO.