Noah Webster is one of the "Christian Nation" crowd's favorite founders to quote, because in the 19th Century, many of his words seem to support their ideal. Yet, as Tom Peters noted on this page, almost all of those quotations come from after 1808 when "Webster underwent a profound religious conversion that changed both his politics and his religious outlook." He "bec[a]me skeptical of democracy, distrustful of government, and far more sympathetic to an alliance between church and state."
Before that time, most importantly when the US Constitution was being framed and ratified, he supported separation of church and state along the lines of Madison's and Jefferson's understanding of the concept.
I've never studied Webster's religious beliefs in detail. I know that in the 1800s when he was saying the things that David Barton et al. like to quote, he was a devout orthodox Christian. Perhaps his political change of mind was precipitated by a bona fide religious change of mind and before that he was, like America's key founders, a theistic rationalist.
[For the rest, see here]