I train a couple of pitchers in my spare time.
MLB doesn't really know the "cause" of the injury. There are a ton of contributing factors. Mechanics, innings thrown, velocity of the pitcher. Some try to tie it to the growth of travel baseball for youth and teenage players. The level and amount of play for young players is higher than ever with a population of players that are chronically undertrained. Some have tried to say the long term effects of throwing a lot at a young age isn't realized until a player is older. Some point to increased average velocity in MLB. The MLB average fastball velocity has increased a little over a mile an hour in the last several years. It doesn't sound like a lot, but, that sort of increase at the very top level of the game is something relatively new.
The real "growth" in TJ has been in youth baseball. Not enough time off, playing year round and players that are very undertrained contribute to the increase in the amateur game in my opinion. Here are some quick numbers....
Tommy John surgeries by year (MLB players only)
2014 - 16
2013 - 19
2012 - 36
2011 - 18
2010 - 16
2009 - 19
2008 - 18
With the exception of 2012 there has not been a big upswing in the actual MLB. When you factor in all levels of minor league ball, every level of college ball, high school and youth baseball TJ surgery is a nice little industry. I know two kids that have had TJ surgery in the past year, neither a full time pitcher.
One thing I have noticed is there seems to be a rash of injuries in spring training and early in the year and then it slows greatly most years. This, to me, speaks to how baseball tends to train and manage its players.
One thing that really confuses the issue of cause is the pitching motion itself. It is a very individualized movement pattern. It is also (throwing a ball 90 + mph) the most explosive movement in all of sports. There is tremendous stress put on the shoulder and elbow. The estimated strain on the elbow at maximum arm layback when someone throws 90 mph is about the same as hanging a 40 lb weight from your hand with your arm layed back.
I have definite thoughts about amateur pitchers, as for pros, already performing at a high level I think it is maybe the cost of doing business. Like sprinters dealing with chronic hamstring issues or football players dealing with knee injuries.