Paine appears to have made his religious leanings well known before the revolution, and it is submitted that "a majority of the founders turned on him" because of those beliefs. Thomas Jefferson was president at the time, and appears to have publicly supported it, so Paine wasn't alone in that regard.
And for the radicalism which came from them. His behavior became more that way as time went on; of course his sniping at Washington the hero would result in a loss of friends...why wouldn't it? Also as I said, his overt support of the French Revolution embarrassed most. Jefferson also was famously in favor of the French Revolution so he was probably closest to Paine in his more radical beliefs.
Only 6 people attended Paine's funeral. He was obviously no longer as popular as he had been because his behavior and indiscretions had gotten worse over time.