First, I am going to totally disagree with you. In my dynasty (take a look at the stats on my tarheel page in the dynasty section), I can run the ball most of the time. So what I am thinking is that you are taking a "hit" by running the type of plays that give you a Negative Bonus. If you take a look at your playbook, there is formations that depending on your OC/DC that works best/worst for your team.
Also, this is not EA's NCAA, where you are going to get 100 yds each and every game. Sometimes I get the tough yards and am happy to finish with 80 yds and the win. Playbooks are the key, as you just can't line up and run the ball, unless you got the personnel, and knowing what plays work best for you.
Sorry you can't run the ball....but you got to go deep in your playbook and find what works and don't work for personnel. I have set up at least 6 play books that I use, after I scout the other team and find one that works best for there defense. Last year, I had the WR's to open up the running lanes to spread the field. This year...I have had to rely on my OL, and some games I just can't run. Also, if you have a bad OC/DC your progression will suffer game per game.