John Proctor's frank confession to Reverend Hale in act 2 is important in that it reveals a lot about the respective characters involved. In relation to John, it shows us that he's a decent, honest man who, for all his faults as a husband and a Christian—he can't recite all of the Ten Commandments; tellingly, it's the prohibition against adultery that makes him come unstuck—still takes his faith seriously. He refrains from going to church, not because he's giving up on religion, or even due to personal animosity towards Parris; it's because he regards Parris as ungodly, as not a true Christian man. This reinforces the suspicions we've already begun to harbor concerning this devious, hypocritical individual. It also tells us that there's nothing genuinely Christian about the Salem witch craze.
Hale's evident sympathy toward John's concerns reinforces the idea that it was possible to be a devout Christian in Salem and still have doubts regarding the wisdom and justice of what was happening.