Paine was well known and, for the time, well read. His book The Age of Reason sold 25,000 copies and had 18 printings. He was not an atheist, but a deist - roughly corresponding to nature-as-God - he strongly believed that the idea that God's ways were 'mysterious and unknowable' was crap - an idea designed to concentrate power to a few. He believed in transparent morality - no mystery required.
As the century drew to a close, Paine was reviled by the colonial religious establishment and many of his countrymen and abandoned by many of his closest friends as a wave of fundamentalism swept the over the nation. Jefferson, notably, stuck by him. Franklin, pretty much an out and out atheist, warned him not to poke Christianity in the eye. In the end, Paine's funeral was attended by fewer than a dozen people.
It wasn't until the mid 1800s that historians began to resurrect the great man and revolutionary that was Thomas Paine. Prior to that, the influence of Paine's books was falsely minimized.
Even today, when you here evangelical zombies channel their fantasy versions of the founding fathers and their mythical guiding faith, you somehow never hear Paine's name mentioned.