Most of the criticisms are voiced by John Proctor and might at first glance come across as criticisms of the church only, but if the audience keeps in mind that the church was the community or society in Proctor's time, then it is obvious that Miller is identifying common human conflicts through Proctor's comments.
1. First, when John and Elizabeth are alone at the beginning of the act, Miller uses their stilted conversation to represent many marriages in American society--forgiveness is rare; conversation is forced, and affection is scare. While it is true that Proctor was unfaithful to Elizabeth, Miller uses the two to illustrate how cold marriage can be.
2. When Rev. Hale arrives at the Proctor household to "examine" the Proctors' Christianity, John uses their "interrogation" to identify problems with Rev. Parris and other members of the community. First, Rebecca Nurse has been arrested, and John is flabbergasted by this news. He sees this as society's way of putting aside common sense for unsubstantial evidence or heresay. Secondly, when Rev. Hale asks John about his church attendance, John tells him that he doesn't go to church because he can't pray in the church. He is so disgusted with Rev. Parris's materialistic (golden candlesticks) and hell-fire preaching. Miller uses these comments to show that society is often concerned with the exterior rather than the inner workings of man's heart.
Secondly, society's greed which pits neighbor against neighbor is clear in Act 2. Mary Warren, Cheever, and even Rev. Hale bring news of neighbors accusing neighbors or witchcraft, and their intentions are obvious--get rid of other landowners so that they can buy up as much land as possible.