This analysis is as flawed, or more, than the worst of the atheists that he is kvetching about. He is critiquing "...a particular kind of atheist — arrogant, argumentative, and intellectually incurious." He is complaining about "New Atheists", of which there are few examples. No doubt there are such atheists, but they don't represent the majority of atheists. But when it comes to discussing religious persons, he makes it a major point to stress that not all religions are defined by fundamentalists - so he compares reasonable religious persons with only the most extreme of atheists. This is a disingenuous comparison.
More important, the author does not understand what atheism is. While most atheists also oppose the foundation of religions, that is not the focus - atheism is the lack of belief in a supernatural deity, the lack of belief in God. There are many religious atheists, and non-religious theists. He also makes up and mixes up arguments used by atheists, for example claiming that the main focus of atheists is religious texts. This is false - atheists will point out that we don't need religious texts to define our moral values, but that is in response to theists who insist that you can only live a moral life if founded on those religious texts. The "moral values clauses" are only a piece of the debate, a minor point for atheists, a major point for theists.
The story is full of logical fallacies. His description of Tyson's example is false reasoning. Tyson said "if" the goal of the death penalty is deterrence, you would have to prove the death penalty deters crime. The author claims that is false because conservatives don't care whether it deters crime, only that we get "justice". That is a logical fallacy, a poor application of reasoning. Tyson's logical response would be, OK, then, if justice is the goal, show how the death penalty achieves justice. Tyson's reasoning is perfect, the author's is flawed. Not to mention that he purports to speak for all conservatives, and ignores the fact that there are other people in our society other than conservatives.
This article is just another in the recent rash aimed at bashing atheists. And just as misinformed as the rest of them.