Well, I think you're hitting it on the head. QB rating is a stupid stat that only measures passing & it also takes into account, in part, the percentage of touchdowns per pass attempts.
If you have a decent running game & a great defense then there should be less reason & opportunites to pass as you play a ball control offense. If you're in a ball control offense of this type with plenty of rushing TDs then of course your QB rating will be lousy.
I'm no big McNabb fan but I probably couldn't find five NFL quarterbacks I would take before him.