John and Elizabeth Proctor are not only physically distant from one another, but they are also emotionally distant. At the beginning of Act 2, John enters the house and is seen on stage by himself. Elizabeth is not a cheerful woman; so John "halts for an instant when he hears her singing" (Stage directions at the beginning of Act 2). John also seems to look for problems with Elizabeth. He takes the opportunity, while she is absent from the room, to taste her cooking, and he "is not quite pleased."
The first words of Act 2 also show the discord between the couple. When Elizabeth enters, she immediately wants to know why John hasn't come home earlier. She questions,
"What keeps you so late? It's almost dark."
The audience knows from Act 1 of the relationship and conversation between John and Abigail Williams. It is obvious from Elizabeth's first words that she, too, knows of her husband's affair and is still suspicious of him.
Additionally, John doesn't eat with Elizabeth. She watches him eat, looking for his approval. Their conversation is stilted and about harmless topics (their son's trap, the crop, a heifer).
After the first section of dialogue, the stage directions again stress the physical and emotional distance between them. Elizabeth's back is turned to John, and
"a sense of their separation rises."
While the two live together, they're simply coexisting.