(More precisely, New Atheists struggle against a specific kind of religion. Human language is somewhat fluid, and people attach words to concepts willy-nilly, without philosophical precision; the word, "religion," is no exception. We are, on the whole, pretty clear about what kind of religion we object to: the idea that God exists, imposes moral duties, obligations and prohibitions, on human behavior. Given that a metric assload of people actually use "religion" to mean just this idea, our use of "religion" to denote the exact same idea does not seem at all confusing or ambiguous.)
I don't even know what "fundamentalism" really means. It has an ostensive definition: when attached to Christianity, "fundamentalism" just means all the things that that Christians use to distinguish self-described "fundamentalists" from "non-fundamentalists." (Similarly, mutatis mutandis, for Islam.) As a New Atheist, I am not particularly interested in theological disputes. Analytically, though, fundamentalism is used in three main ways, to denote the idea that someone believes:
- X is true and worthy of promulgation
- Some text should be taken literally
- X is inerrant
I am a fundamentalist in all three senses. I believe that communism, atheism, evolution, anthropogenic climate change, are all true and worthy of promulgation. I might change my mind that one or another were true, but today I think they're true, and worthy of promulgation. Everyone does this. I do not object because Christians believe something is true; I object because they believe Christianity is true. I believe that my textbooks should be taken literally, not metaphorically. When my economics textbook describes a relationship between the quantity of hats demanded and produced and the price of a hat, I believe they are talking literally about actual hats, actual dollar bills (or euros, etc.), actual factories, and actual people buying and wearing hats. Again, I don't object to Biblical literalist taking something literally, I object that they are taking the Bible literally.
The third meaning is a little more subtle. I believe the data are inerrant, but I want to be very careful about what I mean here by "inerrant." Inerrant does not mean veridical. Inerrant means that if the data appear contradictory, I must repair the contradiction by altering my belief about something other than the data. For example, if I am weighing bricks, and I my scale reports the weight of a brick as 1012 kg, then I have a contradiction between my experience of putting the brick on the scale and the scale. I cannot resolve this contradiction by denying the data: I cannot deny that I lifted the brick, and I cannot deny that the scale reported 1012 kg. I must resolve the contradiction by changing my beliefs not about the data but about the world. Perhaps I performed the measurement incorrectly. Perhaps the scale has changed so that it is no longer measuring weight or reporting the measurement in the same way it was a moment ago. There are, of course, a lot of elaborate ways scientists use to resolve contradictions in the data, but the one way that is absolutely forbidden is to say that because the data contradicts my ideas about the world, the data does not exist or should not be taken literally. (I cannot, for example, say that the scale is measuring the brick's happiness.)
In a deep sense, I mean exactly by the inerrancy of the data what Biblical literalists mean by the inerrancy of the Bible. They do not mean that if there is an apparent contradiction in the Bible, that the proposition is both true and false. Instead, they believe that they must add an interpretation that resolves the contradiction. Similarly, when the data from the double slit experiment contradicted data from our ordinary experience of of rigid objects, we had to add quantum theory to our interpreation of the world to save the data. No matter what our a priori ideas about the world happen to be, if the data contradict those ideas, it is the ideas that must change, not the data.
The change in focus of anti-atheist polemic* from religion to "fundamentalism" — when it is not just outrageous lies and (thanks, Dr. Coyne!), and Dr. Loretta Graziano Breuning is a flat-out liar) — seems at best confused and at worst intentionally misleading. We object to "fundamentalism" only to the extent that "fundamentalist" something-bad is usually worse than "moderate" something-bad. That something bad is, in the sense noted above, religion.
*I do not object to polemic per se. Obviously, I believe that specifically anti-atheist polemic is incorrect.