Think of the running game like a boxer's jab. You're not throwing the jab to knock the opponent out; you're using it to set up the big right-hand shots that lead to knockdowns. When you run the ball early and often, defenses have to respect any and all play fakes, thus spawning bigger plays in the passing game off play-action passes. The running game sets the table for devastating vertical strikes.
There's even more benefit to running the ball in today's game, with more teams gearing up their defenses to get after the quarterback.
http://www.nfl.com/news/story/0ap300000 ... per-effect