3 things that caused this loss, and you already stated them.
Zach Thomas - nothing more needed on that. But that said, Hendrickson is easily their best pass rusher. Somehow the Bengals can keep AD in check (mostly) by scheming for him. Why the hell did we not scheme to help Thomas out on their best pass rusher? Lucky Stafford escaped without injury here and it would have been on the coaches.
Tutu - I saw zero clear evidence that his heel touched. Don't they say that we need clear obvious evidence to overturn a call made on the field? How did they determine that? What I saw was he tip toed and his heel not touch. Utterly ridiculous.
Run Game - Seriously McVay? Against arguably the worst run defense in the league we barely even attempted to run, and, ironically, when we did, we averaged nearly 6 yards.... but yeah, lets have the oldest player in the league (who missed a majority of last season hurt) drop back 40+ times with perhaps the worst LT in the league trying to block their best pass rusher. Makes sense.