On the surface level, Mary Warren is John Proctor's employee and he is paying her to take care of his household while his wife recovers from her illness. When Proctor initially runs into Mary at Reverend Parris's home, he comments on the fact that he is paying Mary to be at home and chastises her for neglecting her duties. As the play progresses, John has other motives for preventing Mary from leaving their home and traveling into Salem. Once John discovers that Mary is an official of the court and is one of Abigail's followers, he becomes furious and forbids her from traveling into Salem. John knows that the witchcraft rumors are false because Abigail told him the truth, which is why he does not support or trust Salem's court. He also wants to distance himself from Abigail as much as he can. John may feel threatened by the fact that Mary is his servant, who is now working closely with Abigail. John does not want Abigail to influence Mary in any way or use her to get back with him. Once Ezekiel Cheever arrives with a warrant for Elizabeth's arrest, John realizes that Abigail is attempting to get rid of his wife and understands that he must have Mary Warren on his side.

John Proctor is naturally suspicious of the rumors of witchcraft going on in Salem and wants to shieldhis family--Mary Warren included--from the repercussions he assumes will follow. Proctor also knows that the children, many of whom are close friends of Mary Warren, are at the center of the accusations and led by Abigail. Proctor fears what sending Mary Warren into town might do and he is fearful of her being sucked into the swarming hysteria that Abigail has fueled around her.

John Proctor initially sees the trials as nonsense and wants nothing to do with the trial.  Additionally, he doesn’t want his family to have anything to do with the trials and Mary Warren, being his house servant, is included as part of his household. When Proctor finds out she has gone he is furious at her for disobeying his wishes.

Proctor may be opposed of his household getting involved with the trial because he doesn’t want his adulterous past to be revisited. Abigail is at the heart of the trial, and he believes her intentions are bad.