If we look at the first chapter of Book the Second, we can see the almost comic nature of the relationship that Jerry Cruncher enjoys with his wife. It would be comic if it weren't so disturbing in the way that Jerry treats her. He throws his boots at his wife as punishment for the crime of "flopping," which in reality is when she says her prayers, and then insists that she is praying against him when she does pray. No matter how much she tries to plead her innocence against this charge, Jerry has clearly decided that his wife is both antagonistic towards him and towards their son, as the following quote demonstrates. Note how Jerry just will not accept any other version of reality from the one that he believes to be true:
You weren't. And if you were, I won't be took the liberty with. Here! your mother's a nice woman, young Jerry, going a praying agin your father's prosperity. You've got a dutiful mother, you have, my son. You've got a religious mother, you have, my boy: going and flopping herself down, and praying that the bread-and-butter may be snatched out of the mouth of her only child.
He calls her a "conceited female" and turns his son against her as well. Clearly, Jerry believes that his wife is trying to work against him and not with him, and his treatment of her is therefore in accordance with this belief. He sees her as working to oppose him and as a barrier to the goals he is trying to achieve.