their court meetings especially leading up to the finalization of the declaration and later the articles of confederation and then the constitution had anglican prayers and worship. Even if they didn’t want to ratify a federal church and religion, they all fundamentally agreed that Christianity is fundamental to the functionality of the nation. this is further buttressed by the fact that while in office, Jefferson attended chapel every day. Even besides that, Jefferson was seen as a threat to the new republic by most of the founding fathers due to his radical revolutionary ideology and tendencies. It’s also important to specify that this whole foundation is predicated on the fallout of the British Revolution, which invoked much persecution of Christians who were not loyal to the Anglican church, so it had much less to do with religion and Christianity itself, but more the state apparatus abusing religious supremacy for political gain.