There are a number of insinuations and accusations made against John Proctor's faith.
The first accusation against John Proctor is that he does not attend church services regularly. (He says that this is because he does not enjoy listening to Reverend Parris complain and does not like Parris generally.)
Not all of his children are baptized. (Proctor defends his position by saying that he does not believe Reverend Parris to be holy and would not like Parris to touch his son.)
Proctor works in the field on the Sabbath day. (Proctor defends his position by saying that his fields failed to produce well for years and only recently have begun to show promise of increasing yield. If he does not do the extra work, he will not be able to see the increase; to feed his family.)