Hitting balls to a tennis player who doesn't have a partner and throwing batting practice isn't training with the team -- those things are necessary. It is not necessary (and wrong) to run with the team.
I know a ton about the sport and human nature. A coach running beside a kid while he's running a long run is a fun killer and motivation killer. Kids have watches, and it doesn't take too long to know how to pace yourself (hit paces given to you by your coach). No one likes a micromanager, and for good reason...keeps them from growing as people (as athletes in this case).
Just because there are coaches that apparently run with the kids on your kid's team doesn't make it right, because it isn't. A good program doesn't have kids in it that are struggling...expectations are set at the beginning of the summer, and either the kids run all summer or they don't. Then, when fall arrives, those kids that didn't run need to start off running slower and shorter than those who did. Good coaches are upfront about that fact back in May...that you will either not be able to keep up with the normal workouts or you will get injured, and you sure in h*ll won't be as fast as you could have been.