A lot of Chipotle CEO Steve Ells' Senate testimony a few months ago in favor of the Preservation of Antibiotics for Medical Treatment Act reads like ad copy, but when you've set up a big fast-food chain that mostly uses naturally raised meat, you've earned the right to boast. More Chipotle-style fast food and less McDonalds-style fast food would be tastier and better for animal welfare. (McDonalds, incidentally, once owned a majority interest in Chipotle, but sold it all in 2006 to focus on their core business.) I haven't thought very much about the factory-farming antibiotic-resistance issue in the past, something it has in common with banking crises pre-2008 and giant oil spills pre-2010.
I guess the only real criticism of Chipotle that comes to mind is that I'd like to see smaller portion sizes made available, but that's mostly on behalf of other people. I'm a pretty big eater, and back in grad school I'd often eat two big meals a day, one of which was a burrito bowl. It's pretty high in sodium, too, but a drinking man needs his electrolytes.