The New York Times is running an interesting series on voluntary religious accommodations -- mostly statutory exemptions for religious institutions and individuals from generally applicable laws, exemptions that are not mandated by the Free Exercise Clause. One tidbit from the first item struck me:
An analysis by The New York Times of laws passed since 1989 shows that more than 200 special arrangements, protections or exemptions for religious groups or their adherents were tucked into Congressional legislation, covering topics ranging from pensions to immigration to land use. New breaks have also been provided by a host of pivotal court decisions at the state and federal level, and by numerous rule changes in almost every department and agency of the executive branch.
The special breaks amount to "a sort of religious affirmative action program," said John Witte Jr., director of the Center for the Study of Law and Religion at the Emory University law school.
Professor Witte added: "Separation of church and state was certainly part of American law when many of today's public opinion makers were in school. But separation of church and state is no longer the law of the land."
Now I think there are quite good arguments against religious-specific exemptions that end up giving special treatment to religious institutions and individuals that's not available to comparable nonreligious institutions and inviduals, though there are also often good counterarguments. It is this skepticism about favoritism for religion that led the Supreme Court, for instance, to read the conscientious objector exemption from draft laws to apply to people who have deeply held nonreligious philosophical objections to war as well as to those who have religious objections.
But note how unhelpful the appeal to separation of church and state is here. The exemptions discussed in the story generally involve the government's decision not to apply various regulations and restrictions (various child care center regulations, employment discrimination laws, financial disclosure laws for charities, and the like) to religious institutions. A few involve exemptions for religious individuals, but most involve religious institutions.
Such decisions to leave church free from state regulation, it seems to me, are separation of church and state, at least under one plausible definition of "separation." It is abolishing the affirmative action for religion, by applying laws to religious institutions the same way it's applied to other institutions, that would bring church and state closer, here in the sense of having the state have more authority over the church. In fact, one form of "separation of church and state" that many "separationist" judges and legal scholars have urged is (1) discriminatory exclusion of religious institutions from many generally available government-run benefits (such as school choice funds), but (2) preferential exemption of religious institutions from many generally available government-imposed restrictions (such as many aspects of employment laws, historic preservation laws, and the like).
Of course, one can define "separation of church and state" to mean "the state ignoring people's and institutions' religion and religiosity, and treating everyone equally regardless of their church affiliation or lack thereof." This would mean (1a) evenhanded inclusion of religious institutions in generally available government-run benefits, (1b) prohibition on preference for religious institutions in such benefits, (2a) evenhanded application of generally applicable laws to religious institutions and people (though perhaps with some exemptions to some laws for all conscientious objectors to that law, whether the objection is religious or secular philosophical), and (2b) prohibition on laws that single out religious institutions and people for special burdens. Some judges and legal scholars have endorsed this view, though generally without calling it "separation." (My view comes close to this one, though with a few exceptions that I don't want to dwell on here, since this post is about the phrase "separation of church and state" rather than about any particular legal proposal.)
One can also, I imagine, define "separation of church and state" as "discriminatory exclusion of religious institutions from generally available funding programs, but evenhanded coverage of religious institutions and people in regulatory programs." That seems an odd definition to me, but who can say for sure?
My point here is that "separation of church and state" is more a slogan than a well-defined term. Though it seems to me that it should cut in favor of such "affirmative action" programs that exclude religious institutions from generally applicable burdens, obviously others use the term diferently, and the term is capacious enough to be used differently. And on top of that, even those who take the first view of separation that I described -- exclusion from some benefits and exemption from some burdens -- have to explain just where they draw the line: Few, for instance, would bar the police or fire departments from investigation crimes or putting out fires at churches, or would bar cities from providing the same tax-subsidized sewer access to churches as they do to all other institutions.
So when you hear talk of "separation of church and state," keep in mind that this term by itself isn't much of a well-defined legal concept (such as, say, "probable cause," "strict scrutiny," or even "freedom of speech," as defined by the Court's decision) or a clear philosophical concept. It's generally a slogan, these days probably mostly a means for rallying people with a certain set of attitudes about religion-and-government issues, not a helpful tool for analysis.