My husband and I drove through Mexico in May 2009 with our two medium dogs. We found bed/breakfasts were much more willing to allow us to bring our dogs in our room - but not most other hotels/posadas. The smaller the place - the more mom/pop run the place - the more likely the dogs could come inside with us.
The no-tell hotels are frequently called "Auto Hotel" as part of the name on the sign. We didn't actually stay in one, but have friends who have frequented them as a convenient, inexpensive, and nicely appointed rooms. Many are on the outskirts of town and right on the highway - so no so good for walking dogs. But the plus side is that you drive into a garage, the door is closed and you walk into your room. Maximum stay is 12 hours - so you need to make sure that you don't pull in to early in the afternoon, or you will have to leave way too early. Plus, walk the dogs before you pull in.
As far as attitudes by Mexicans about large breeds - I lived in a town with all sizes of breed dogs including Mastiffs, Dogue de Bordeauxs, Bouviers, St. Bernards, shepards, etc. If your dog is well behaved - no one cares. If you pick up after your dog - no one cares. You may get a lot of people wanting to take photos when you are out with your dogs because it would be unusual to see 3 large dogs at once - but I don't think anyone will be fearful as long as your dogs are not barking, growling or lunging at the end of the leash towards people or animals. Well behaved dogs make excellent citizens no matter where they travel.
Dog Food: You can typically find something like Science Diet at a vet's office. In the grocery store - you will usually find Purina products. You will likely spend quite a bit more for dog food down here due to the shipping/import costs associated with dog food - and especially since your dogs must go through a lot of food compared to my medium size dog that eats one tuna can scoop of kibble twice a day.