Ben Levi: I checked the Pirush Hamshnayos that you mentioned. It is a very long introduction to “chelek’ with some very interesting discussions on many matters of “emunah” but I digress.
I read (and re-read) the section that you are alluding to and I do not read it at all as you did. The Rambam does divide the people into three groups when it comes to understanding chazal. The first ,those who take everything exactly as it is said. (A group that,incidentally, he is not too complimentary about). The second group who dismisses “divrei chazal” if they do not understand what they mean and thirdly, the very few who understand that divrei chazal have hidden meanings. I don’t think the Rambam dealt with any natural scientific fact at all. You misquote the Rambam when you write that “they think they know reality better”.Nowhere does the Rambam say this. He says that they dismiss sayings that they think are erroneous. Incidentally, the Pirush Hamishnayos was written in arabic and what we have is a translation,hence one cannot deduce too much from its wording. The Rambam, I think, talks about a saying like, for ex.: that Yaakov Ovinu is not dead (chelek). The first group will take this saying as it is said; Yaakov Ovinu is not dead, without understanding that there is a hidden meaning to it.
The second group will dismiss it as totally erroneous as, after all, they embalmed him and buried him! The very few who know will understand that the “maaamar chazal” should not be taken as it is written but that there is a hidden meaning to it.
Nothing what the Rambam writes here has anything to do with the matter that we are discussing.