Waknuk is an extremely intolerant society ruled by religious extremists that believe that if you are not built in God’s image, you are blasphemous. This is the result of some kind of cataclysmic event in the past that they have determined was God’s wrath. They are determined to prevent another such occurrence.
One example of the lack of acceptance of anyone different is Sophie with her extra toes. She and David are sitting peacefully one day when another boy sees Sophie’s footprint and finds out her secret. After that, Sophie has to flee to the Badlands. David is horrified. He asks her parents if they couldn’t have done something when Sophie was a baby to protect her.
'Mrs Wender, if it's just Sophie's toes, couldn't you have cut them off when she was a little baby? I don't
expect it would have hurt her much then, and nobody need have known.' (Ch. 5)
This is a perfect example of how extreme this society is. The fact that David would even suggest chopping off a baby’s toes to save it, and that such an extreme move would not even save her, is frightening.
David’s father is the enforcer of the religious doctrine. For this reason, Sophie’s parents do not want him to go with them when they try to get Sophie out, because they are worried that he will make things worse for them. His father is an extremist.
David, concealment of a Blasphemy -- not reporting a human deviation -- is a very, very serious thing. ... It is everybody's duty to report any kind of Offence to me – even if they aren't sure -- so that I can decide. (Ch. 50)
David’s father is violent and abusive. He is a religious tyrant who beats his son for having contact with—and hiding—what he considers a Blasphemy. In Joseph Strorm’s world, there is no middle ground. There is no tolerance. He turned away his own brother, and would turn away his own son. This is why David goes into hiding. He brutally beats him now, but that is only the beginning.
In this society, anything that does not match the image of perfection that the people have set down as Godly is eliminated. Crops and animals are destroyed, and people are cast out. Fear of an apocalypse drives them to extreme intolerance, even son to father.