John Proctor was very much an individual, his own man and an independent thinker. He detested Rev. Parris and viewed him with complete contempt. John recognized Parris's vanity, greediness, and selfish nature. It grated on John, a hard working farmer, that Parris seemed most interested in wringing every penny he could get from his congregation--including the deed to the minister's house and golden candle sticks for the church. When John's religious habits were questioned, especially in regard to his youngest son's not having been baptized, John said that he saw no "light of God" in Parris and did not want the minister's hand on his baby. Instead of going to church, John spent his Sundays working his farm for the good of his family.
We might also infer, perhaps, that John avoided church because of his guilt over his adultery with Abigail Williams. Until the very end of the play, he saw himself as a terrible sinner, a man with little goodness in him. Going to church under these circumstances would have made him feel very hypocritical, no doubt.