Along this line another much-vaunted philosophical relic is the presumption of atheisim. At face value, this is the claim that in the absence of evidence for the existence of God, we should presume that God does not eist. Atheism is a sort of default position, and the theist bears a speicial burden of proof with regard to his belief that God exists. So understood, such alleged presumption seems to conflate atheism with agonosticism. The assertion, "God does not exist" is just as much a fact claim as the statement, "God exists." As a result the latter claim requires justification just as much as the proponent of the latter. Absence of evidence is not evidence of absence.
I would only add, regarding yours and others statements as to how do we know, we examine the world to discern the truth of metaphysics in exactly the same way the scientist does. We do not rely on sociological imput, paternal teachings, psychological evaluation...we use philosophical tools and induction to evaluate for truth. Scientific inquiry has its own set of presuppositions. It relies on logic, reason, rational thought, numbers, sets, (all are metaphysical in nature or have a metaphysical nature qualia). These are the same tools we use to in examining for proofs of the existence of God. Plantinga refernces natural law and the basicality of knowlege of God as a starting point, and he makes a very good case for it (don't be too quick to write off that notion, but that is another story entirely).
This is only the general application of the null hypothesis which is used within science to minimize the number of false positives (Occam's razor and all that). It is very useful for winnowing competing models; but it lies open to the systematic weakness of false negatives.
Plantinga is very good at discussing the philosophical difference between physics and metaphysics: in particular, much of what underlies the scientific method is metaphysics which originally derived from Christianity; now that the "general" regularity and (shall we call it?) "categorizability" of the Universe is well understood, many pretend that such regularity is not only reasonable on its face, but well-nigh inevitable; thus undercutting (in their mind) the "need" for a Creator to "explain."
But in doing so, they in fact are making serious metaphysical errors which are not apparent to non-philosophers; they pretend in response that as long as they can more or less accurately predict the behaviour of nature with their models, then their metaphysics doesn't matter, or have been substantiated after the fact.
I may need to write an essay on this and one or two related topics...