When your view is one giant assumption

One of the difficulties I've encountered when arguing with materialists (or scientism disciples, as I like to call them) is how they treat science and reality as if they are the same thing.  Or to put it in another way, to doubt the scientific method is to doubt reality.

A big disclaimer before we continue, I do not doubt the scientific method.  As I type on this computer about to publish this post (not to mention that I am a software developer by trade) I am all too aware of modern science's contributions to the health and well being of society.  Even though it was actually PEOPLE who did these things, and not science itself.

I have detailed before the issue with scientism, specifically the position that science is the only reliable method of inquiry.  But the intent of the discussion is not to dispute science, only to recognize two important observations:

1. That science, properly speaking, assumes a boatload of metaphysical assumptions.  
2. That those assumptions, taken to their logical conclusion, provide a pretty good framework for the existence of God.

But the problem with a lot of encounters I've had with materialists is that one of two things happens:

1. The scientific method is essentially dogma and a half.  No question will be permitted, period.
2. The attitude that if we examine the scientific method with any critical thinking, we have to throw reality out the window.

The inability to turn a critical eye to science itself undermines a great many claims that materialists are "free-thinkers".  Far from questioning everything, the materialist swears unyielding fealty to the scientific method.  To analyze the method is to doubt, and to doubt is verboten.

The main problem is that the scientific method is ultimately a reasoning process.  Scientific claims are highly specific, and requires experimental verification given the number of assumptions in play, the specific claims being stated, and that claims about nature herself are involved.  

Ultimately the scientific method is only as strong as the claims used to support it.  Since scientism folks do not have any methodology for testing such claims, the whole thing is balled up under "science" and assumed outright.  Far from engaging in critical thinking, the modern scientism-ist is one of the worst practitioners of fideism.