Chipotle: great carnitas, guac, and I can get a beer if I dine in. If you look at the contaminated food cases and where they're happening, it's pretty obvious the culprit is a bad produce vendor for those affected regions. Sure, not properly cleaning/cooking can contribute but if it were a company wide issue it would be all over the country and it isn't.
Taco Bell: I'll throw my work behind what others said- if you're legitimately getting sick then you might have some sort of allergy or condition. Otherwise you're probably lying and just want to get in on the tired old diarrhea joke.
As with all fast food it's all about quality control and staffing. I've seen brand new shiny stores open up, but they quickly turn to shit because you can tell they just brought over all the shitty employees from a nearby location to run the new one. If the regional managers don't care either then it never improves.