I notice articles by atheists tend to run in themes: "Islam is bad, so religion is bad," "Science disproves religion" and so on. One of the recent themes is on Thomas Jefferson and his calling for a "Wall of Separation," citing the Danbury Letter.
The key point of this letter is:
Believing with you that religion is a matter which lies solely between Man & his God, that he owes account to none other for his faith or his worship, that the legitimate powers of government reach actions only, & not opinions, I contemplate with sovereign reverence that act of the whole American people which declared that their legislature should "make no law respecting an establishment of religion, or prohibiting the free exercise thereof," thus building a wall of separation between Church & State. Adhering to this expression of the supreme will of the nation in behalf of the rights of conscience, I shall see with sincere satisfaction the progress of those sentiments which tend to restore to man all his natural rights, convinced he has no natural right in opposition to his social duties.
The argument tends to be "Jefferson said we need to keep a wall between Church and State. Religions are trying to change laws. Therefore religion needs to be controlled."
The problem is twofold. First, the Danbury Letter is not legally binding document or the like. Second, the modern interpretation is one of bifurcation: "Either we control religion or religion controls us," which simply is not the case.
The letter Jefferson was responding to (from the Danbury Baptists) expressed a concern that certain sectarian groups might seek to attack members of the government being "irreligious," based on their own views. Now this is a legitimate concern. Certainly Catholics in Maryland in the 17th and 18th century before the founding of America knew of groups which, once in power, sought to strip them of their rights to religious freedom which they granted to others. However, we remain with the problem of a wall of separation properly understood.
Now the first amendment to the Constitution does tell us:
Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances.
This means of course that the state may not impose any specific religion on the people true, but it also forbids the prohibiting of the free exercise of religion. It seems the dangerous part of Jefferson's letter is when he says:
I shall see with sincere satisfaction the progress of those sentiments which tend to restore to man all his natural rights, convinced he has no natural right in opposition to his social duties
The dangerous part of this sentiment is this potentially opens the door to the negation of the First Amendment if misapplied. It's not completely wrong of course: The Church holds that freedom is not license to do what we wish, but rather the freedom to do what we ought before God, for example. The problem is when the state decides a certain group acts contrary to undefined "social duties" not because of actual acts which are unlawful but because they practice a religion which is not well received.
As the old saying goes, Quis custodiet ipsos custodes? If the state defines what is intrusion on the Establishment of Religion, what prevents it from defining social duties in such a way to harass a religion or the like?
This is the problem of the modern understanding of the separation of Church and State. The claim is that something benefits religion in general is a violation of the separation of church and state. The problem is such a view de facto defines religion as being in opposition to social duties when it speaks out against the state.
We do need to remember that the view of atheism also falls under this criteria. The atheist who seeks to remove public expression of prayer or the like is in fact violating this so-called wall of separation in a way which denies the rights of the first amendment.
The atheist who wishes to cite the Danbury Letter as excluding religion from political life needs to remember that the first amendment also grants to citizens the rights of the freedom of press, speech, to assemble and to petition the government for redress of grievances.
This of course means that a Church has a right to speak out in word and in print about the ways the nation is bringing harm to members or harm to itself. Yet churches do not have this right. If a church wishes to say "What this government official is doing is wrong," they cannot without legal repercussions.
It is a paradox of course set about by a phrase with no legal bearing. Separation of Church and State means a state cannot dictate how an individual may practice religion or to infringe of the practices of a religion, and certainly this is what popes like Leo XIII praised about the American way. However, on the other hand, going from "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof" to "Religion shall have no say in government" is certainly a contradiction, because it denies or limits members of religion their right to free speech, press, assembly and redress.
Things like the Danbury Letter or claims like saying "The Founding Fathers were not Christians" is in fact a Red Herring. Certainly the Declaration of Independence shows that the understanding of America had some understanding of God, who had an authority above the state:
We hold these truths to be self-evident, that all men are created equal, that they are endowed by their Creator with certain unalienable Rights, that among these are Life, Liberty and the pursuit of Happiness.
In other words, these are not rights the state can arbitrarily give and take away. Rather they are things people possess which are beyond the ability of the state to regulate. We now come to a problem with the claims of the atheist over America. If we do not hold that our rights come from a creator, from what do they come from? What makes them binding so that tomorrow Obama cannot say "I'm taking away your right to the free press"?
The choices for where our rights come from are: God, or Nothing. If they come from God, then no person can take them away from us… certainly a government can compel us so we cannot exercise our rights, but in doing so, they act in an unjust manner.
However, if they come ex nihilo (out of nothing), they are not rights, but tolerances from the government, as what one man can say is good for him, another might disagree with. One government administration might decree we have the right to property, another which follows the first might claim we exploit people by the existence of private property and it may not be allowed.
Some atheists and agnostics do not like where this leads. They recognize that some actions are wrong, but reject the idea as the source of what is good, so they seek to find a source which is not absolute to give us these rights, such as instinct or some undefined sense of justice.
The problem is our rights are only as absolute as the source which grants them. What binds a nebulous force like "justice" or "instinct" to do something we must obey? What part of it prevents a Hitler or a Stalin from saying "I reject these values and replace them with another which I find superior for me."
Either we recognize that our rights as human persons come from a binding force outside of us (which, if one does not call it God, must define what it is) or we are forced to concede that we have no rights at all, but merely the tolerance of a government.
This latter view of course would be against the Constitution, and this is the paradox of Jefferson's Danbury Letter