I think I know what you're getting at, in that a lot of atheists will defend their points through the use of a scientific method.
But I don't think that atheism has a direct link with science.
People can just reject religion through personal interpretation.
I've seen science work both ways - atheists can learn science and feel comfortable in that it can be used to explain what's happening around us and why it's happening. On the other hand, though, some people could be theists through science because they see how beautiful science is and gather that our natural laws must have been put in place and designed by something of superior intelligence.
As for myself, I have never really believed in a God because I found it all slightly absurd, somewhat silly.
My passion for science came long after I decided against God. So for me, there was no link between the two initially
Yeah, i've come across quite a few atheists (some at this site) that justify their atheism through using the scientific method (which starts with the presumption of what is basically a closed system of that which is being observed). Simply because the method assumes a closed system (without which, observation would be 'affected'), does not have any grounding on anything outside the field of observation (which is why scientific observation is usually more accurate when using a smaller and more specific field of observation)...
I myself always believed in a God because I found the idea of atheism to be pointless and stupid. But I guess I became interested in science because of my belief, and the framework that it presents to my thinking about my observation of the world.
While I would argue that the evidence or observation of science is theistically neutral, I would argue that the interpretation of such evidence is according to the method through which the framework of science is placed within a world view.
For example, an atheist could look at a feather and think "This feather could have emerged through successive generations, increasing in it's 'featherness' from a scale of some kind." While the theist could look at the feather and think "This feather shows remarkable suitability for the purpose of flying, structurally it could only have been designed this way." While the observation is the same, the interpretation of the fact is dependent on the framework.
So yeah, basically science has nothing to do with theism/atheism, but that the interpretation of any evidence presented by scientific observation is affected by the framework in which that evidence is seen. An objective matter is observed, then interpreted through subjective means.