When you show me the atheists protesting "Muslim" week in CA public schools, Jewish and Muslim holiday decorations on public land in Palm Beach, Florida (as well as other pockets around the US), and start expelling students who wear a Muslim headscarf to school, than I will agree with your criticism about the author making assumptions about what atheists think. Because it seems all their efforts are focused against one religion, I think a good argument could be made for the author being on the right track.
Well, if the Pledge of Allegiance said "Under Allah" instead of "Under God", I think those atheists would take a little more interest in suppressing Islam. But that's not what it says.
Obviously, the reason why some atheists in the U.S. have a bone to pick with Christianity is that it is the dominant religion in the U.S., particularly if you count Catholicism and Protestantism as one. And that dominance is reflected in our many traditions.
So while I don't agree with the efforts to strip God out of the public sphere, there is a rather easy explanation as to why the focus seems to be on Christianity. Extensive layman's psychoanalysis is hardly necessary.
I think a good argument could be made for the author being on the right track.
I suppose so, but he hasn't made it. As I said, I'd say I'm probably roughly on the same page as him with regards to his central objections. It is his attempt to explain atheists and their beliefs that I find lacking.