There are two big things going on with religion in The Autobiography of Benjamin Franklin: Franklin's attitude towards organized religion/attending church, and his belief in God. For him, those things are really separate. In this text, being religious isn't about attending church, donating to pastors' plans, or observing what are sometimes seen (by Franklin) as arbitrary rules. Instead, it's about believing in God, praying honestly, being virtuous, and doing good works. Franklin's kind of mystified by the different religious people he comes across (Quakers, Moravians, Dunkers), and doesn't subscribe to any of their customs. He's all about communicating with God in his own way, according to his own systems.
Despite his arguments against organized religion, in explaining his belief in God and the pious practices he follows, Franklin shows himself to be as, if not more, observant as traditional "believers."
Franklin's Autobiography presents many practitioners of organized religion in a poor light, showing them as more focused on following specific tenets and practices – in other words, concentrating on observing their particular customs – than on really working on ideas of virtue and humility.