Rights of Conscience
Opponents of church/state separation say that it's a myth foisted upon the American people by militant secularists bent on oppressing Christians and removing all hints of religion from the public square. They imagine that abandoning the concept would usher in an era of renewed morality as we allowed God back into our schools, prominently displayed His Commandments on our courtroom walls, and acknowledged the Biblical principles on which this nation was founded.
The fly in this particular ointment can be summed up in a simple question: "Whose Biblical principles?" Anti-separationists either never ask themselves this question, or assume that their own principles (being obviously correct) must prevail.
This ignores both history and current reality. If our founding documents enunciate a religious principle, it's not the Biblically exclusionary message of the First Commandment ("Thou shalt have no other gods before Me") or the Gospel of John ("no man cometh unto the Father, but by me"); it's the freedom of conscience protected by the First Amendment's "free exercise" clause. As Thomas Jefferson wrote:
The error seems not sufficiently eradicated, that the operations of the mind, as well as the acts of the body, are subject to the coercion of the laws. But our rulers can have authority over such natural rights only as we have submitted to them. The rights of conscience we never submitted, we could not submit. We are answerable for them to our God. (Notes on the State of Virginia, 1784)
On top of this, modern American society is probably the most religiously diverse the world has ever seen, with adherents not only of the major (and minor) monotheistic faiths, but also Buddhists, Hindus, pagans, agnostics, atheists, and who knows who else. Any government entanglement with religion is bound to affront, disadvantage or even oppress large numbers of these people.
And, as it turns out, you don't have leave the friendly confines of Christianity to find such effects. As the Washington Post reports from Jackson, Mississippi:
A Christian adoption agency that receives money from Choose Life license plate fees said it does not place children with Roman Catholic couples because their religion conflicts with the agency's "Statement of Faith."
Bethany Christian Services stated the policy in a letter to a Jackson couple this month, and another Mississippi couple said they were rejected for the same reason last year.
You can chalk this up to simple ignorance among the people at BCS; according to one of the rejected couples, their priest reviewed the statement and saw no conflict with Catholic teaching. But it's hard to imagine that a Christian who would discriminate against Catholic applicants on religious grounds would hesitate to discriminate against Jews and Muslims, much less Buddhists or Secular Humanists.
It's also hard to imagine why any government funds at all should be going to support this kind of nonsense.
(A tip of the cap to atrios for the pointer to the Post article.)