A) Cheese is not usually expensive, like avocado, and so not usually considered worth paying extra for
2) Cheese is known not to be healthy, and part of the appeal of Chipotle is the illusion that you're eating healthy food
3) A different kind of cheese is already available for free, so that substitute good is bound to drive down demand for queso
I did notice that they recently cut corn tortillas and one (or two?) of the meat options, so they at least seem to be cognizant of the benefits of reducing decision fatigue by concentrating on their best-selling options