I fail to understand how a story about human small-mindedness becomes a story about how there is nothing other than a material universe.
[WS:] I think that many, if not most atheists, who on average tend to be more intelligent and educated than the religious folk, have a far more sophisticated concept of "material" than "dirt and stone." For example, the concept of energy, which is not directly observable is still a part of the material realm, whereas the religious folk are likely to see it as a part of the supernatural. Likewise, the concepts of probability, multiple causation and interaction effects, positive feedbacks, nonlinear relations (e.g. a mouse giving birth to a mountain or vice versa) are all part of "material" causation to atheists, while the religious folk tend to anthropomorphize these relations as the will of the supernatural. In short, materialism is not the same as primitive sensualism and smart aleck empiricism.
I think that the main bone of contention in the religion debate is not really ontological - i.e. whether an entity called 'god' exists - but sociological i.e. what are the socially acceptable sources of knowledge. Most of the religious folk tend to be deeply anti-intellectual: they are highly suspicious of- or altogether reject science and expert knowledge. Consequently, they put high trust in the fundamentally non-scientific form of knowledge, such as faith, revelation, intuition, folk wisdom etc. which by their very nature are antithetical to science and scientific methodology.
Stated differently, religiosity, especially in the US, is a manifestation of deeply seated anti-intellectualism, and has nothing to do with philosophy or even theology. In fact, US religiosity is deeply anti-theological and focused mainly on ritual and sensual manifestations. This anti-intellectual thrust is obviously resented by the people who are its main target: intellectuals, experts, or even people with the enlightenment-style rational outlook on life. It is also interesting to note that in Europe, where this anti-intellectual populism is rather weak, the relationship between religion and science is much more harmonious and center on philosophical debates instead of kulturkampf.
So to answer your question, small-minded anti-intellectualism is the leading tenor (albeit not the only voice) in US religiosity, and that fact alone polarizes the public debate on religion. It provokes extreme reactions on both sides, which includes combative "go get them!" attitudes and making strong ontological and epistemological statements and hyperboles about the nature of the universe and human knowledge of it. In a more rational and balance society, however, such radical, combative positions would not be warranted, and the debate would like take a more reflective and philosophical deliberations about the nature of the universe, human knowledge, ethics, etc.
Wojtek