This was the point of the "opposing views" article I referenced above.

The First Amendment has repeatedly been interpreted by the Supreme Court to mean that Churches are free from taxation, since taxation, by definition is a form of governmental control, and the First Amendment calls for, as you quoted, "no law respecting an establishment of religion or prohibiting the free exercise thereof." If you tax churches, you violate the first amendment because you are now, "prohibiting the free exercise thereof."

This is something that's been upheld by the courts repeatedly. If you have a problem with this, you literally have a problem with the First Amendment. So go ahead, hold a Constitutional Convention, and re-write it.

As far as the Charities are concerned, I counted at least 15 religiously affiliated charities in the first two pages. I'm not going to go through and list, line-by-line, the religious status of all 200 charities for purposes of brevity.

And true, my quip about atheists worshiping the state is a bit of a generalization, the point of me saying this is to point out that most atheists simply aren't consistent in their rejection of hierarchy. For most, they simply replace a religious hierarchy they find distasteful, with the State. Thus, they pay tribute to the state (and get mad at anyone who doesn't). They attack anyone who attacks the existence of the state. They cheer when the state chooses to smite their enemies (and go to great lengths convincing it to do so). And they find security in the state (which is why we see a greater demand for state-funded education and healthcare).

Tribute. Loyalty. Dogma. And a sense of Security.

If that isn't a kind of worship, what is?