In the Yucatan Peninsula, I believe that the issue with drinking the water unfiltered is not the bacteria, etc., but that the water is full of minerals that can result in kidney stones. The city water in Merida is treated. I would think that would be the case in QR as well. I've not had any issues with the water, but occasionally eating a heavy, rich meal can have me hurrying to get home. But, then that happens to me in the US as well.
In that part of Mexico it is extremely hot and keeping well hydrated will keep you much healthier, whether it is city water or bottled. Enjoy your stay and visit a farmacia if you experience any ill effects. They even have doctors at some of the larger stores. They will fix you right up, and vets are everywhere to take care of your "babies".
