I live near ancestral puebloan country and have spent quite a bit of time backpacking there and reading about their cultures (as best as you can since they moved away and their culture was impacted in big ways by other tribes and Spanish/American colonization after that). The first thing of note that is that they did not have any large domesticated animals. Turkeys are all that you hear about but surely dogs were also there. Large wildlife was also surely not a problem because man was one of their bigger predators.
One interesting thing to note is the puebloan art style depicts people with these big torsos, broad shoulders, and stick figure legs (see link below). Nearly everyone, which I think is fascinating. I obviously don't think that was how they were built but it is interesting that it matches up with how their doors were shaped. Was that the unrealistic body image that their culture idealized? Did that somehow impact their architecture? Doubtful, but an interesting thought.
Another thing that you'll notice in this region is the high prevalence of granaries and their meticulous construction to keep rodents out. Minimizing the entrance at ground level may have helped slightly with keeping mice out of their rooms. Similarly, it would reduce the amount of snow blown inside during winter.
Mostly though, I bet it just made sense with air intake/venting combined with passive solar heating. Maximize the venting of smoke while reducing the drafting of colder air at floor level as others have said. With regard to solar, these homes are almost exclusively built on south facing rock alcoves. The summers are very hot and winters can be brutally cold. During th winter months, the sun is low enough to shine under the alcove and radiate the homes while in summer they stay mostly shaded. For those that aren't far enough recessed, greater shade at floor level would help with that since it would be the first to get sun.
