This is a common misconception that many theists hold as it relates to atheism. Atheism isn't a rebellion against theism. Atheism is skepticism at its roots, and theism has yet to present evidence to overcome that skepticism. If theists were able to bring forth strong evidence then atheists would gladly join them, including Shermer. Atheism isn't an argument against theism, but a lack of a supported argument for theism.
It seems to me that creating the specter of "New Atheism" is an attempt to reinforce this misconception. Theists try to create the picture that New Atheists have all of the trappings of religion in order to create some sort of equivalency when the real situation is much different than that. The specter of New Atheism plays well to the choir, but it doesn't really address the reality of what is really being argued, IMHO.
Culturally, the middle ground appears to be secularism and democracy. As Churchill stated, democracy is the worst kind of government, except for all the others. We landed on secularism and democracy because it appears to work the best. While both sides of the debate can argue ideology, we also need a pragmatic solution to the real problems we have today. The idea that the people have a voice in government and religion should remain in the personal sphere is the most pragmatic solution we have found. I tend to think of it in terms of sports. The rules of baseball are secular. They don't require a belief in that god or this god. You don't have to belong to a specific religion to play baseball. The rules of baseball are the same for all religions or no religion. We have decided that our laws should do the same because it seems to work.
I think the same applies to science. There are plenty of theists who are scientists, and they are great scientists. The rules of science are secular in the same way that the rules of baseball are secular. That isn't to say that you can't believe in God in order to do science, only that you are required to follow the rules of science, which are enshrined in the scientific method. That's the idea that Shermer thinks is worth protecting and supporting, and I think that is also true of many theists.