Colby Cosh further discusses the constitutionality of the Congressional chaplains.

His closing paragraph is the clincher:

Mr. Ehrbar's last point brings us into the question of the right approach to take when continuous, standing practice conflicts with the principles in the documents. I believe the Lincoln view on this has outlasted the Douglas one, for better or worse.

Colby's comparing religion to slavery -- a Marxist device, no? -- but that's not the thrust of his post. The question is, does the maintenance of chaplains conflict with the principles of the founding documents? More precisely: what rights does an atheist have under the "free exercise" clause?

None, in fact. The atheist has the right to free exercise of his lack of religion. He does not have the right to object to anyone else's practice of religion. Nor even to require that government money not be spent on obtaining religious services for government employees -- any more than I, a Catholic, can demand the expulsion of Protestants from the chaplaincy.

There is no prejudice to the atheist's right to stand on the streetcorner saying "There is no God" -- this is covered by the first amendment right to free speech. But the atheist has no special protection for the practice of his atheism, because you don't have to do anything to be an atheist.