It's hard enough to run the ball with a bad run blocking OL and zero good run blocking TEs (Brown is only made to look reasonable as a blocker in contrast to the absolute zeros that are Henry and Gesicki in this regard), but when you add to the equation just how much teams are comfortable playing Cover 1 and just loading the box with zero fear of the passing game, it's pretty much impossible. Teams can just run Cover 1 Man and erase the Patriots running AND passing game, it's kind of insane.
The only solution would be to just go under center more often, run more play action and see if that scares linebackers from crashing down instantly as you drop to hand the ball off. Right now they just don't throw when under center. My feeling is they'll be under center more often if the game is low scoring and they aren't trailing from the jump, which could help the running game, but even then my defensive approach wouldn't change. I don't think this team is capable of generating big plays even in traditional play action (outside of some very specific trickery like the Pharaoh Brown TD).