I'm going to guess based on the article and other comments that it's not so much "no one" is eating Chipotle as much as "fewer people than before" are eating Chipotle. Certainly there are people still going for the food, but I think the issue is more that there was a sizable drop that is reflected in the finances.
I would imagine this sort of issue is one where it's easy to miss the forest for the trees. I was never really a fan of Chipotle to begin with, but wasn't bugged when I heard about the outbreak; it just seemed like a tradeoff in my mind for less processed meats - you naturally expose yourself to dangers like this. I wasn't aware that the fans of Chipotle thought differently, but apparently they did and I guess the chain mishandled the PR on the event?
tl;dr - the two differences between buying raw chicken breasts and cooking them yourself, and buying precooked premade chicken meals and heating them.
One of the things that Chipotle used to (and still, to some extent) do differently was that they turned raw meat into cooked meat onsite, rather than taking precooked frozen meat from central facilities and reheating it.
(They also purportedly have very stringent guidelines about what they permit to be done to the animals the meat comes from; I don't know what those requirements are, so I can't say how strict they are.)
The tradeoff with that, combined with their local sourcing guidelines, is that they'd have far more distinct pipelines and places that they needed to ensure a lack of contamination in.
The article covers them having now switched to an approach which opponents refer to as "precooking" the meat in large central facilities, to kill pathogens effectively, while also maintaining as much of their "fresh food prepared right in the restaurant" ethos as they can muster.
(Not being a chef, it seems like they basically cook the meat to something like medium-rare, slowly, but at sufficient temperature to kill pathogens, and then cool it and cook it the rest of the way at restaurants.)
It's not necessarily a raw numbers issue, although that may still be a contributor. It's a branding issue, and the article does a pretty thorough analysis of the subject.
It's all about discretionary, discerning, conscious customers who would think to themselves "Chipotle is fresh, wholesome, and healthy, and they have integrity" or something of the like; now there's fewer people who associate this with Chipotle in particular. Some of the beneficiaries of this development are Panera and Qdoba, who still evoke a similar thought.
It may still be the case that Chipotle draws decent crowds, but they are drawing those crowds for different reasons -- promotions, people in a forgiving or adventurous mood, or people who simply don't care about the ethos very much and just want some tasty fast casual food.
I work close to the Empire State Building -- following the health scare, the lines were way shorter during prime lunch hour. I've noticed them come back but seemingly not in full force (even with the Chiptopia rewards, which we did take advantage of at work).
Yeah, the few times I've been, it's not been bad but there's still people eating there.
I go rarely due to price really. Once I started fixing food at home, I realized I could make the same stuff to bring to work for a reasonably better price. Salsas are really the only thing I need to learn to try my hand at.
