Well, human arms aren't designed to throw a baseball overhand 250 times a game (Rounded off estimate for a starting pitcher who throws 120 piches in a game, plus 81 before innings, and then warm-up in the bullpen and playing pitch and catch before start.) So, it's an unnatural motion on an unstable joint as it is. Softball pitchers can throw a lot more because throwing underhand is a more anatomically natural motion. Just because of that, sometimes teams can have a rash of pitcher injuries- for example the Cardinals with Carpenter, Mulder, now Piniero out with some type of injury, as well as a couple of relief pitchers.
Now that I have defended the trainers a little bit, when you have players with injuries like "sore shoulders" and hamstring pulls that last for months, we probably need to look at how we are doing our stretching programs with our players- particularly our pitchers after games. We also probably need to look at our techniques for reducing inflammation after a start. Those would be the first two places I would look if I was Jay Logan, our trainer.
Another thing that I think might be affecting our pitching staff is our pitching coach. For example, I read on here that someone said that Crosswhite's pitching motion looked totally different. I noticed while watching Greg Houston pitch on Maroon to the Max that his pitching motion looked different than last year. As far as pitching mechanics are concerned, in theory the better your mechanics, the less chance you have of an injury. However, some people have pitching motions that, while not mechanically perfect, work best for them. For example, Dontrelle Willis. Also, sometimes if you change someones pitching motion, you actually may put them more at risk for an injury. When you change someones motion, you're forcing them to use muscles that either have not been used or have not been used in that way very often, and that puts strain on the arm. Also, sometimes pitchers change their motion a little bit if they are hurt. A good example of this is Dizzy Dean, who altered his motion after hurting his leg in the All-Star game.