I think that the author's main message in this play is that people should be aware of how much we can get swept up in hysteria and what bad things can occur when we do. He is saying that we tend to lose our heads when we are afraid of something.
In the play, the people of Salem lose their heads because they are afraid for various reasons (that Miller explains in the notes). Because they are afraid, they fall for the silly stories made up by Abby and her friends.
Miller is warning us that we tend to persecute people when we are afraid. Hysteria hits us and we forget our better natures and turn on a convenient scapegoat.
One of the primary messages of the play is how government can move away from the interests of the many and become a force to serve the agendas of the few. The government depicted in Salem is without any type of check or institutional limitation. People who are accused by it are without any sort of significant recourse nor can they engage in any authentic defense of self because the government has become a tool of the powerful few, exerting its magnitude on the many. In this setting, the body politic is more afraid of accusation than anything else, preventing any sense of community and collectivity being formed. Miller's warning seems to be that individuals must be willing to take a stand when their government is operated in a manner that is contrary to public interests. There has to be some level of check or boundary that individuals are able to place on it when it goes awry in such a manner. Little hope can be present if individuals are afraid of accusation and willing to accept such a condition through silent complicity.
One of the author's messages has to do with the idea of the theocratic society, a society in which church and state are not separate. The theocratic nature of the Salem society means that moral laws and state laws are the same; sin and the status of one's soul are matters of public concern as they can threaten the public good.
All of this then leads to the other themes of the play, namely hysteria, intolerance, and the importance of reputation.
I think that Miller's main message in "the Crucible" is how governments can abuse their power as both the senator Joe Mc Carthy and the accusers in the play only accused for their own gain, power being the obvious reason. Also he could be saying that both the accusations of the 1950's and those of 1692 were unjustified as the main accuser (Abigail Williams) was found to be untrustworthy when she stole money from parris and ran away. So maybe Miller is steriotyping all accusers of the 1950's to be like Abigail Williams.