On twitter, Chris Coxen asked me about the recent strikeout article that ESPN did. You can see it here but I'm sure you've heard/read something similar elsewhere.
The gist of it is "batters strike out too much, that's why runs are down" (though they do touch on what I'll go through below) It's not that simple. Working the count is good. Starters are usually better than relievers, certainly better than middle relievers, and effectiveness does decrease as pitch count increases. So work the count and get the starter out as soon as you can.
The problem is that the purpose of working the count has been perverted. You should be working the count to get on base and the effect on the starter is a very nice secondary effect. Players now are working the count in order to get a pitcher out of the game and getting on base through a walk is no more important than it was before. The end result is a more pitcher friendly counts. Given our love for the all or nothing hitter that means a lot more Ks. Sure home runs are increasing (or more accurately staying high) but creating more outs is more detrimental than hitting home-runs is helpful (at least at the rates they usually happen).
More outs + same men on base = less runs. Regardless if you can hit a few more bombs out of the park.
(Graphs over the last 31 years 1982-2012)