Sometimes, you just get beat.
I'd like to see some stats/snap counts, because to my eye, we played more base this game than any all season. I also saw a lot of Bear/46 fronts within the base personnel grouping. IE, both guards and the center covered up by our three down linemen. I also saw several snaps with both Martinez and Goodson at ILB.
I didn't keep track of bringing a safety down into the box--that might have been the only other obvious adjustment that could have been made, but maybe the already did it?
The next move you can do to stop the run is calling slants and other stunts to get into the backfield. IMHO, that's playing into the Shannahan/zone scheme hands. If you're slanting, the cutback lane opens up further. And you can take yourself out of the play easier.
From what I could see, the linemen didn't necessarily get beat. They made (most) of their hay going wide. They got bodies on bodies, won their battles, and Martinez/Goodson couldn't fight through the trash to clean up the play.
A run plugger DT and upgrade ILBs probably would have made the game a little more fair.