Methodological naturalism is the basic approach of science. Since science is the study of the natural world, the methodology of science is limited to the parameters of the natural world. Methodological naturalism is theologically neutral.
So what does that mean?
On a very fundamental level, it simply means that science is the study of the natural world, and, therefore, science is limited to naturalistic methodology. Science is limited to the observations of matter, energy, space, and time.
Another way of putting it is that science has no preoccupation with anything that is super natural. Science is limited to a focus on the natural world. Science doesn’t bother itself with anything but the natural world (though scientists might stray beyond it).
None of this should be in the least bit earth-shattering. Confusion arises, however, when we begin discussing the supernatural, the metaphysical, the theological, and even the philosophical realms in relation to science.
There are those scientists, for instance, who have recently suggested that the advance of science today has done away with the necessity of philosophy. People like Lawrence Krauss and Neil deGrasse Tyson have made statements like that, though they have both backed off of those initial statements more recently. It’s important to understand that those statements, themselves, are philosophical in nature, and not scientific.
To suggest that science has done away with necessity for philosophy is to ignore the limitations placed on science in its very methodology. Science, itself, is not philosophical, but evidence from science can support premises that are philosophical, and scientists themselves draw philosophical conclusions from scientific facts.
Science may inform philosophy, but it can never replace philosophy. To think otherwise is to exalt science beyond its natural parameters (pun intended) and to fail to appreciate the difference between science and philosophy.