Precisely because it was well-known that the First Amendment was meant seriously. As the Treaty of Tripoli says, signed by John Adams, one of the Founding Fathers who definitely was Christian, as ratified by the Senate:

As the Government of the United States of America is not in any sense founded on the Christian religion;

Effectively, secularism and pluralism were still, at that time period, radical 'liberal' ideas that many conservatives were not onboard with. I mean, shit, Jews were still kept in ghettos in most of Europe, and in most places only Catholicism or (generally a specific strain of) Protestantism were accepted, rarely both. Whoever heard of a country that wasn't founded on GOD!?