There's quite a few reasons we haven't run the ball more actually.
1) As mentioned, we fall behind..usually early
2) After we have relative success early running the ball, teams cram 8-9 guys in the box and focus almost solely on our run. Notice how we have a penchant for the 0 to 1 yard runs. Teams completely sell out against our run because they know our QB can't beat them through the air.
3) Beanie Wells said in a radio interview last week that the game against KC is the first time he's been healthy since the preseason.
4) Tim Hightower's fumbilitis. (Although I will say he seems to protect the ball better now; Perhaps he wasn't getting more runs until he could earn Whis' trust back)
5) LSH has been banged up and isn't, even when healthy, going to carry the ball much.
6) And lastly, if we had a QB that could just simply go through his progressions and throw with the slightest bit of accuracy, we wouldn't have opposing teams putting much emphasis on our running game. My word...we have a wide open receiver on almost 95% of all our passes and either DA overthrows him or doesn't see the open receiver at all.
Just as the "threat" of a running game can open the passing game up, conversely, the "threat" of a passing game can open up our running game. Right now, we severely lack that "threat" when it comes to our passing game