James Madison, principal drafter of the First Amendment, thought that it prohibited Congress from hiring chaplains, and the President from proclaiming Thanksgiving Day. His thoughts on the subject are here.
He has a good point, but he never claims that he is the authority on the Constitution but that it was the product of many and that the final authority lies in it's ratifiers- which many (most?) of those in the congress that voted for the chaplains were.
There may have been sound reasons for saying that that still don't apply to the current case. Madison defined religion (correctly) as "the duty which we owe to our Creator, and the manner of discharging it" - that is, the prayers, the rituals, the hymns, etc. Certainly chaplains and thanksgiving are part of that definition. But merely making a statement regarding the source of moral law is not, in itself, religion. It's simply a view of the way the world works, without which no human institution can properly function.