They point out that John has not been faithful in coming to church and that he works on Sunday. For Puritans, who based much of their ideas about others on appearance, John's actions would have been incomprehensible. John has legitimate reasons not to be in church. He does not trust Parris and sees him as a greedy, self-serving minister; John thinks that he is fine in God's eyes as long as he has a relationship with Him. This does not satisfy the Puritans; they want to see others doing good works. In truth, they donot care much about one's heart attitude; so no matter how much closer John Proctor might have come to truly worshipping God over the regular churchgoers, it carried no weight in his favor because no one witnessed his "worship."
Parris and Cheever know that the judges follow the same legalistic religious rules that they do; so John's irregular attendance and apparent disregard for the 4th Commandment would most likely count against him in the judges' eyes.