Dan's points about quality of pitching are very good. Let me recap:
1) Overall, your batters are facing better pitchers than they do in real life. The 2.1/1.9 Jaime Navarro-types are often squeezed off the roster. This is particularly true, say, for the first 60 games or so when managers will go w/ their best rosters before either a) burning out low-inning/high performing pitchers; or b) decide to bag the season and bring up a roster of INNs.
Better quality pitching will deflate hitting stats somewhat.
2) In the short run (say, the first two times through your division), you're likely to face either a lot of good pitching or a lot of bad pitching. Pitching (and talent) doesn't seem to be equally distributed in leagues; you got your crummy staffs on 3-4 teams in a division, you got your quality staffs on 3-4 teams in a different division. So, if you're facing 4x2 pretty good staffs over the first 15 series, you're going to see hitting stats depressed. THAT should even out as you make your way to the less impressive rotations.
Kurt