I don’t know where the idea that pitchers need to be world-class distance runners came from, but it is complete and utter nonsense. Some cardiovascular conditioning for pitchers is beneficial, but not at the expense of power. According to research cited in the NSCA book, Essentials of Strength Training and Conditioning, excessive aerobic conditioning has an adverse effect on power and strength. This means that every time a coach makes his pitchers run long distances, it is essentially subtracting MPHs from their fastballs and making them less effective.

Think this guy has a decent fastball? I doubt it.
Many coaches subscribe to the notion that “good” workouts end with their pitchers exhausted and on the verge of vomiting. Again, this is pure, unadulterated crap. The only thing these types of workouts are good for is breaking down the muscles in a pitcher’s legs and making them weaker. Good trainers and coaches will prescribe exercises that challenge the athlete but never make them ill.
Another thing to watch out for as a pitcher is overtraining, which is “a physical, behavioral and emotional condition that occurs when the volume and intensity of an individual’s exercise exceeds their recovery capacity.” Essentially, your body is unable to recover fully in between bouts of exercise. This means you will plateau in your fitness gains and eventually will lose strength.
I saw the effects of overtraining firsthand last season among the pitchers on my team. As a team, we usually only got one day off every two weeks. In addition to practice and games, we would also meet as a team 2-3 times a week to lift weights. And of course, there was the pitchers’ conditioning. This conditioning took place after literally every practice and game, and consisted of nothing but long-distance running (poles, loop around campus, etc.) As the season progressed, our pitchers were getting more and more run-down and were suffering on the mound as a result. Towards the end of the season, velocities were decreasing and ERAs were soaring. Of course, to the coaches this meant that the pitchers needed to be punished by doing the very thing that had led to their problems: more running. With ignorant training philosophies such as this, we were doomed to fail in postseason play.
If your coaches require pitchers to do ungodly amounts of running, you should try to get them to do some reading about the harm that it can cause. You don’t want to piss your coach off though, so be polite and discreet about it and you may be able to get him to change his mind about the effectiveness of sustained aerobic exercise.
For more information, Dan has already written about how to effectively train as a pitcher here: A Few Words About Pitchers’ Conditioning