I'd feel far more comfortable with Chipotle if they could definitively say, "It appears uncooked cilantro in our rice was harboring E. coli; we've changed how we prepare that item and believe the problem is fixed." Instead, we now have a nebulous "central kitchens work for other companies, so now we're doing it" solution. As little as I cared about their feel-good "local food" drumbeat, it bothers me that they turned away from that stance.
At the same time, I've not seen a slowing of the constant level of decline in cleanliness at the stores near me. When they were opened, they were shiny a new. Now, though, they've begun to attract a noticeable level of crud in the corners and other hard-to-clean areas like the perforated wooden wall boards. The kitchen areas look to have received a good once-over, but the stores show the abuse they've suffered under high-volume visits.
What if people aren't sick from bacteria in the food, but from a nasty colony on the underside of a table or chair or even wall leaned against while waiting to order food that is often eaten in handheld form? Does the food safety program encompass those areas too? If so, why doesn't it clearly show?