Chris didn't really hate his parents; in fact, going by his letters (all sent before he vanished from their lives) he still loved and respected them. However, he felt trapped by their insistence on living within societal boundaries; he felt that they were pawns of society instead of individuals, and so their influence restricted him from pursuing his own goals.
Both father and son were stubborn and high-strung. Given Walt's need to exert control and Chris's extravagantly independent nature, polarization was inevitable... He brooded at length over what he perceived to be his father's moral shortcomings, the hypocrisy of his parents' lifestyle, the tyranny of their conditional love.
(Krakauer, Into the Wild, Amazon.com)
The similarity between Chris's personality and that of his father was one of the problems; similar people tend to grate on each other, especially when one is in direct authority. Chris felt that his parents, while meaning well, didn't understand the ideals that he had learned from Tolstoy or Thoreau, and that they were addicted to the pursuit of material wealth just like everyone else in society. Instead of speaking with them and finding common ground, he rebelled in passive-aggressive ways. When he finally started his journey, he resolved to never contact them; sadly, he held to this resolution until it was too late.
He hates his father because his father ha second family with a woman before chris was born and told chris that he and chris's mother met straight out of collage. because of this he had a lot less respect for his father.... :( sad face...