There are a couple of reasons this might be the case.
The favored model in the pass-first game leans toward pass blocking OL players over road graders and (2) TEs valued for pass catching ability over run blocking. Many teams favor zone blocking schemes to accommodate the more athletic/finesse OL players valued for pass blocking over road grading. Many teams look for a primary RB in the Chris Johnson/Jamal Charles mold...they complement the passing game and provide some long gainers (which pad the average by the way), but are a crap shoot in short yardage. Many teams want what was once considered "3rd. down" skills on every down.
The compromise in the pass-first game is in personnel not suited to ground-and-pound. It's gotten to the point where 2nd. and 5 and 3rd. and 2 are predominantly passing downs.
Another consideration is in the hedge-betting in throwing the ball on short yardage. If you run with 2 yards to go, it's an all-or-nothing proposition on opening the hole or cutting a D-Lineman for a dive play. If you play action or roll out, the thinking goes, there's time for the QB to select from a few options among the receivers or run it in.
Certainly there are teams that balance pass/run in their personnel and scheme, either for lack of a decent QB or settling on a game managing option. They are in the minority, however.
If running is more successful than passing in short yardage, yet only 25% of the teams favor it, it's worth considering that 25% or fewer teams run a relatively balanced attack.
