Milkman from an early age has a great deal of respect for his father, though he recognizes he is very much unlike him, and his respect is mixed with fear. Macon Jr. is not a friendly man to those outside of the family, and for his family he reserves a good deal of criticism. He is a domineering man, filled with strength and vigor but also a great deal of anger and disappointment. Milkman finds himself weak by comparison. He has a leg-length discrepancy and cannot hope to ever emulate his father. Though he works in his father's business, there is no sense of shared identity or path forward for him.
Milkman sees himself in figures who are in some way compromimsed or disadvantaged. From an early age, he tries to differentiate himself from his father both in apperance and attitude. This is his first attempt at separating himself from his father and trying to craft an identity that better suits his physicality and temperament. The company he chooses, Guitar and his aunt Pilate whom Macon Jr. has forbidden him to see, is a sort of thumbing the nose at the father, an incipient form of rebellion.
When Milkman enters young adulthood, this self-identification with weakness is replaced with a new confidence in his abilities. The striking of the father is an important turning point for Milkman, as the roles of domineering father and obedient son are reversed. It is now Milkman who has triumphed over the father. This reversal is not without consequences. When he sees his father bested by him, it is a painful realization that the man he once reverenced for his strength, that idealized form of the masculine and invulernable father, is no longer something to be taken for granted.
The sordid story told to Milkman by his father regarding his mother's past shatters Milkman's sense of belonging or having his own people. His identity in the making is compromised, and the need to leave his family and build a life of his own for himself becomes more urgent. The visit to his father's hometown in Pennsylvania is something of a reversal of these sentiments. He sees his father for the first time through the eyes of people who knew him as a child and the love he had for his own murdered father. The way Macon Jr. is described by these older men instills a new sense of pride in Milkman for his father, who he was, and gives him some glimpse into Macon's past. There is no longer a clear split between son and father, and the sense for Macon that he is a completely separate entity from his father is done away with.
On Macon's part, the son is an escape from disappointment. His affection for Milkman appears to be conditioned upon the sorry state of his conjugal life - a sort of using the son as a means of ownership to spite the wife and her history as the daughter of a wealthy man. The whole basis for the paternal/filial relationship then has its origins not in an unconditional love but one based upon pre-exsting circumstances.
The great strength of Milkman in the end is the realization that such relationships can never be perfect, indeed should not be expected to be perfect, because they are relations between people and people are inevitably flawed. Milkman offers the reader the idea that one's relations with one's parents are inevitably of little consequence in who one becomes. There is no dichotomy between the terrible and the good, separation vs reconcilation. One can be both separate and connected simultaneously if one is willing to accept situations for what they are but not attribute too much importance to them.
The work centers on Milkman and his transformation from a dissatisfied youth with little understanding about the larger world and the past that make people are what they are in the present, into a man who has gone out, experienced things for himself, and comes back completely changed in his mindset. It is the prototypical hero's journey, and Milkman's relationship with his father is in microcosm representative of the eternal recurrence of this journey. It is sometehing Milkman's father had, something his grandfather had before him, and so on down the line.