I can't find the link, but I'm pretty sure I read in one of the numerous post-game articles that Watson told Pelini at halftime that they'd run the ball more in the second half and Pelini's response was to just play football. Without reading too much into it, it sounds like Pelini wasn't too concerned with protecting the defense - he just wanted the offense to score points.
If Western Michigan was giving up open looks downfield by bringing the safeties up so they were even with the linebackers - then why run into an 9 man front when you can just throw over them.
I agree that in the heydays of the 90's we ran against 9 and 10 man fronts and had success - but the team has changed and the offensive philosophy has changed. I think we would all agree Joe Ganz is a good enough passer and decision maker to complete a pass when he needs to. In my humble opinion - I agree with Pelini and Watson - why pound the ball for 3 yards when you can just as easily throw it for 10? That's the beauty of the offensive system we're using now.