I agree with all of this. I'm an atheist, so the bottom line is that I think atheism is better than theism. The article is meant to be provocative because atheism is more problematic than many atheists realize.

The problem with theism is that theism is preposterous after the Scientific Revolution. The problem with atheism isn't so much the content of basic atheism, but the implication of that content. So technically it's a problem for atheists (who subscribe to more than just the negative thesis of atheism) rather than for atheism itself. It's a problem for the broader atheistic worldview.