Just focus on the first two sentences. Take the notion of causality. It underlies all of empirical science, yet it is not something that can be proved empirically. It is a given, a built in part of how we perceive things. You can read more about this if you check out the work of David Hume or Immanuel Kant.

There is nothing naive about recognizing that human knowledge is limited by our knowing apparatus. What is truly naive is to mistake the models of science with "reality itself" (a nebulous term)