So traditionally metaphysics was the science of discovering facts about reality through the use of "pure reason". I take metaphysical issues to be things like the existence of so-called "universals", philosophy of time (like whether the past and the future exist in the same way the present does and why does time flow in one direction), what causation is, whether humans have free will, personal identity (what makes a something the same person at different times, what a person is), the ontological status of mathematical objects (are numbers real?) and, I suppose, the existence of God and a bunch of other issues. Now I would say there are all sorts of positions one could take on these issues and if one had good reasons for those positions one would at least be acting rationally even if one was still wrong.

Now its possible to hold positions on these issues for bad reasons. For example, your reason might be that the Bible told you you have free will. But this doesn't distinguish metaphysical issues from any other issue- you might think that pi = 3 because the Bible says so. Certainly you'll agree that there are religious beliefs that aren't metaphysical ones.

Now there is a trend in metaphysics that rejects the existence of supernatural or non-material things (perhaps this is what you meant by metaphysics). But this isn't an axiom. We have reasons for rejecting the supernatural and they're very strong reasons. When it comes to God's existence the reasons are even stronger against existence.