The message of Miller's play is a commentary (and warning) on the tendency of individuals to be persuaded by the opinions of a group. There is a grave danger at the heart of this tendency, one which is borne out in the action of the play.
...rather than take a stand against proceedings they suspect are unjust, the townspeople of Salem go along with the trials.
We see the message clearly in the example of Reverend Hale. He is a man who believes in his own integrity and honesty, but who also forfeits his own thinking in favor of the group. When confronted with the truth about Abigail, Hale refuses to heed his honest doubts and falls into the persuasive trap of "going along" with the group.
At first, Hale fails to realize that he is making a choice. He still believes he is acting with integrity. This is part of the danger of the scenario. People who have the support of a community are allowed to believe in their own virtue and honesty because they are in agreement with the group. To Hale's credit, he eventually realizes the truth of what is happening in Salem.
He comes to realize that John Proctor is guilty of nothing more than adultery yet he lacks the courage to question the decisions of the court and the prevailing attitude of seventeenth century society.
In the example of Reverend Hale, we see Miller's comment on the dangers of the individual's moral thought being subsumed by the moral leanings of a group, a community, or a mob. When the group is the moral authority and no individual can be held accountable for the actions of the group, morality becomes corrupted.
Individual rights and individual moral judgement should be honored and maintained in order to ensure that society has a personal understanding of justice. The alternative, as presented in this play, is likely to be a state-operated, power-based authoritarianism that has little regard for moral responsibility.