It was all from a letter from Thomas Jefferson promising that in spite of what happened in France, he wasn’t going to forcibly outlaw Christianity. I doubt a sliver of those who speak the phrase know the context.
Tom Jefferson was answering a question of a pastor of Danbury baptist Church in Danbury CT had about whether Tom would be allowing a National Denomination of Christianity (a national religion) for the country to which Tom said no, people were to have their own choice of denomination and religious expression. https://wallbuilders.com/separation-church-state/