Aside from his confusion regarding tax exemption v subsidies, which I confess I am not very knowledgable about either, the rest stands up to any test of logic. And the author makes the point that churches benefit from government services such as firefighting, etc., that the rest of us have to pay for. So in a sense, they are indirectly receiving what you might call a "subsidy", since they are being handed free service.

And I personally don't give a shit what the "Founders" intended for churches, as I sure as hell don't feel I should be personally obligated to set aside a special place for someone else's god. I'm sure the founders had many backwater ideas that haven't stood the test of time and progress. After all, we all know how many of them felt about women and slavery.

I perused the list of charities you posted. Most of them did not sound like religious organizations to me. Am I wrong? But even if they are, what about the thousands of other religious organizations who are doing very little to support charity. And what about the author's suggestion? Why not have churches separate their charities from their spiritual rituals? We could just tax those who like to spend their time performing rituals, and leave their charities out of it. Just like all the rest of us, hey?

And then we have this. “Congress shall make no law respecting an establishment of religion or prohibiting the free exercise thereof.” I am not a lawyer or even well versed in law. But I am not so sure that this means that churches are guaranteed freedom from taxation. And even if it does, I think that it presents a glaring flaw in our constitution, as exception to civic duty is clearly unfair to any but those who benefit from it. Even if that statement should mean that we can't tax religious organizations, why shouldn't superrich individual pastors have to perform their duty to their country? And what does that say about those who use their faith to take advantage over their neighbor?

It is not about punishment, artifex, it is about fairness. The author never suggested to leverage penalties against churches, instead he is suggesting they carry their share of the burden.

What's with the dig about atheists worshipping the state? Clearly a sweeping generalization and unfounded. Bad form.