He was gay and repressing it.

He was clearly gay and repressing it.
The storms he kept seeing were the representation of his gay urges trying to take him over.
The visions of others taking his daughter away were the representation of family members trying to rescue her from his gay lifestyle.
His tornado shelter was his fraglle shell of masculinity, his attempt to keep the storms/the gay away.
The oily rain was golden. He was getting a Golden Shower.
The birds represented his penis. Birds have beaks. They peck. Pecker. Penis.
He wanted his friend sent to another supervisor on the job because he knew he was sexually attracted to him and thought things might get hot and heavy if they were both working together.
His wife knew he was secretly gay, and urged him to go to a psychiatrist.
The dog knew he was gay. He was angry that the dog knew, so he 'closeted' the dog by putting him in a pen out in the yard.
Tornadoes are phallic. He saw them as giant penises on the horizon coming towards him. Tornadoes blow wind. Blow. Blowjob.
The townspeople suspected and spread rumors that he was crazy/gay. He then came out to all of them at that town dinner, confirming their belief.
His boss fired him because he was gay. He saw that he stole/borrowed the backhoe to try to cover up his homosexuality.