John, Elizabeth, and especially Rebecca Nurse are all portrayed as good, strong, Christian people. They are not presented as sinless. That would go against the basic beliefs of Christianity. The Puritans in the play are Christians. The audience knows about John's affair with Abigail Williams, and the audience can see that he is truly repentant.
"Abby, I may think of you softly from time to time. But I will cut off my hand before I’ll ever reach for you again. Wipe it out of mind. We never touched, Abby."
John also is an upstanding member of the community, and people know it. He's a hard worker, and he's good to his word. Likewise, Elizabeth is equally respected. John even calls her to his defense, because he knows that she will not confess to a lie even to save her husband.
"In her life, sir, she have never lied. There are them that cannot sing, and them that cannot weep - my wife cannot lie. I have paid much to learn it, sir."
Lastly, Rebecca Nurse is basically the poster lady of the pure Puritan life. When she is suspected of witchcraft is when Hale begins to doubt the entire proceedings. The fact that she would rather die than confess to a lie should tell readers a lot about her Christian character.
Miller uses those three characters to show that evil lies in external forces. He does this by having them punished incredibly harshly despite their proven goodness. Their punishments are not because of any law breaking or sin either. They are punished because Abigail and her cadre all accuse witchcraft. John, Elizabeth, and Rebecca cannot defend themselves because Abigail and her girls are being taken at their word. The only defense is confession, and none of them are willing to confess a lie because Puritans believe that would mean eternal damnation. John, Elizabeth, and Rebecca are being accused by external forces. They can't defend themselves because the court proceedings do not work in their favor. Everything that is happening to them is out of their control. The evil that is affecting them is completely out of their control.