What are 3 metaphors used in the play, "inherit the wind" that represent religion?

I don't know if I can get three. It is important to understand that the play is actually about the supposedly irreconcilable differences between science and religion. 

Two of the 3 central characters, Hornbeck and particularly Brady, are too flawed to represent well science and religion. Brady is a metaphor for all that is bad in religion. He is seen as a bigoted monster. He is overconfident and has a shallow understanding of the world. His wisdom, if he has any at all, comes from his misreading of the Bible. His understanding is further marred by his greed and his desire to win at any cost. 

Hornbeck is no better. He's a walking stand up comic that moves the play along by being the comic relief. It's not part of your question so I'll just move along.

The Title itself is a metaphor for what religion can do. Jeremiah Brown is determined to undermine the truth that is at the core of the play. He goes so far in his denunciations, that even Brady can see that it is too far. Inherit the Wind comes from Proverbs 11:29 and it is well worth quoting that, because both Brown and Brady sow enough discord that they are those who will "inherit the wind." Brown actually does inherit the wind. He is left with nothing. His righteousness is barren and it has left him barren. 

So here are the answers to your question.
1. Religion is seen not as Bert Cates saw it (A comfort), but as something that can lead to an inheritance of the wind.
2. Religion is seen as something shallow as seen through the eyes of Drummand when he studies Brady in the courtroom
3. Religion is seen as mindless when some of the townspeople welcome Brady. 

Sorry. You get my long answer for the night. There is no easy way to answer your question.