What was the author “shouting” to the reader in "A Good Man is Hard to Find"?

This is certainly an interesting question, and you could find textual evidence to support many ideas for what is being shouted at the reader in "A Good Man is Hard to Find." One idea that the author, Flannery O'Connor, could be "shouting" at readers is the idea that people are not capable of knowing right and wrong without God. The evidence for this would be when the grandmother tries to express that Jesus could help the Misfit. He responds:

"Jesus was the only one who ever raised the dead," The Misfit continued, "and He shouldn't have done it. He thown everything off balance. If He did what He said, then it's nothing for you to do but thow away everything and follow Him, and if He didn't, then it's nothing for you to do but enjoy the few minutes you got left the best way you can."

Additionally, O'Connor paints the Misfit as a sympathetic character in many ways, blurring the lines between good and evil. While he has murdered, he also extends social graces and kindness. In this way, he is better than the children who show nothing but selfishness and rudeness.
Another thing that could be shouted at readers is the idea that each generation has thought that the younger generation has become less respectful and has morally declined. The textual evidence for this would be the disrespectful behavior of June Star and John Wesley toward their parents, grandmother, Red Sammy and his wife, and toward the murderer, Bobby Lee.
Flannery O'Connor herself said of her own story that what was most significant about it was the "moment of grace" the grandmother experiences. In her essay "A Reasonable Use of the Unreasonable," O'Connor spoke of the heroine of her story, the grandmother. She is a hypocritical woman who wears her faith on the outside but doesn't let it change her heart. However, at the moment when her death is imminent, she has a genuine change of heart and experiences the power of grace. Here is what O'Connor wrote about the grandmother's experience:

I often ask myself what makes a story work, and what makes it hold up as a story, and I have decided that it is probably some action, some gesture of a character that is unlike any other in the story, which indicates where the real heart of the story lies. This would have to be an action or gesture which was both totally right and totally unexpected; it would have to be one that was both in character and beyond character; it would have to suggest both the world and eternity. The action or gesture I'm talking about would have to be on the anagogical level, that is the level which has to do with the Divine life and our participation in it. It would be a gesture that transcended any neat allegory that might have been intended or any pat moral categories a reader could make.

O'Connor goes on to describe the grandmother's moment of clarity when she realizes she is responsible for the Misfit and bound to him by the bonds of kinship, as are all men. She has been talking about the mysteries of the Divine, but until this point in the story, it's been empty talk. In this moment, she experiences the grace and the mystery of the Divine interacting with the common.