Methodological naturalism, as I understand it, is not a "naturalist world view." It is simply a term that describes a practical and fruitful technique for learning about physical phenomena.

Science involves the testing of hypotheses. In order to be scientifically useful, a hypothesis must make predictions that can be tested and verified by repeatable observations. If a hypothesis cannot be tested and verified by repeatable observations, then it does not qualify as a scientific explanation. That doesn’t mean the proposed explanation is necessarily wrong, just that it’s not scientific.

Science does make a few philosophical assumptions, but they are what most people would consider common sense. For one, science assumes that phenomena are continuous. In other words, in order to do science we assume that the past really happened and that what we observe happening today will continue into the future. Science also assumes that there is an external physical reality apart from our internal consciousness. That’s really about it as far as assumptions are concerned.

Despite claims to the contrary, science does not assume naturalism. In general, scientists do not rule out non-natural explanations a priori. If you can propose a testable hypothesis based on it, then it can be scientifically tested. Indeed, so-called "supernatural" causes have been the subject of scientific investigations (i.e. prayer efficacy studies). However, at this point, "supernatural" causes have not been incorporated into scientific explanations because none of the experiments designed to test them have yielded positive results that were independently verifiable. Of course, if such experiments ever did yield positive results, scientists would most likely drop the "supernatural" label.

Some people say that methodological naturalism is a restriction on science. I see it as more of a description of science. Science is based solely on "natural" explanations simply because the things we call "supernatural" have yet to yield repeatable, verifiable observations.

When investigating an unknown phenomenon, the history of science has shown that a "natural" explanation is the best bet. "Methodological naturalism" is merely a description of the fact that scientists routinely bet on "natural" explanations.