From the very beginning when the Pilgrims came to America the church played a role. Most, if not all, had been persecuted for their faith. They saw America as their last chance to be able to worship God as they believed the Bible taught.
Although initially opposed to amendments, he supported the idea of freedom of religion where the government does not favor one denomination over another. He wasn’t afraid of the church influencing government, but rather government establishing a national religion.