Ancient already jumped all over this, but antibiotics aren't solely used on a case-by-case basis as a specific treatment for a condition. They probably SHOULD be used that way, but they aren't. Especially with stuff like poultry. It's easier to treat them via feed/water en masse if you can, than about any other method I can think of (we did Terramycin this way...foul, nasty yellow powder into their water). And some things were/are marketed as not just a treatment but also as a preventative measure, meaning that many probably overuse it. Also, what he said about the use of low-dose antibiotics is true...it isn't something he just made up.
Now, whether or not it's a health hazard is a debate that is still ongoing, AFAIK. It doesn't bother me to eat anything that was raised with antibiotics, but if there is some substance to the claim that it can lead to antibiotic resistance bacteria, then yeah, I can admit that's probably a bad thing (if true).
Personally I'd file this under"Maybe an issue...maybe...but Chipotle likes to market it to rubes anyways"