From the Biblical view that nature is a legitimate field of study, many make the exaggerated leap to the metaphysical view of naturalism, that the natural world is the whole of reality. Nature is self-contained, self-explanatory and autonomous, without purpose or meaning beyond itself. Thus naturalism rejects any notion of supernatural revelation. The metaphysics of naturalism is always monistic and its ethics, such as they are, can only be derived with ambiguity from physical human nature and experience.
Naturalistic views of epistemology have varied from rationalistic to positivistic, but they always limit knowledge to natural events and relationships. The history, composition and structure of the physical universe are the legitimate subject matter of science, and in the eyes of a naturalist there are no objective sources of truth beyond this. Physics goes the farthest in reducing nature to simplest terms, such as the fundamental particles and fields ("We are all reductionists now.") Stephen Weinberg, Dreams of a Final Theory.
That science has made progress over the centuries no one disputes. In fact the success of this enterprise has led some scientists to become arrogant and insensitive enough to declare that their success is a confirmation of the truth of naturalism. They say that God is superfluous and fictitious.
However, this does not follow. Science can be -- and is -- practiced by many theists, and is consistent with a theistic view of nature (see the details on nature here). In fact, many of the leaders of modern science were believers in God, such as Copernicus, Kepler, Galileo, Newton, Boyle, Faraday, Maxwell, etc. Naturalism is a philosophical, if not religious, belief. Science per se is empirical, but it is not naturalistic.