Obviously, Chris McCandless' relationship with his parents is problematic and complicated. His relationship with his father, Walt, in particular is extremely strained. From the beginning of the book, Krakauer places quite a bit of emphasis on that relationship as the primary reason, or a primary reason anyway, for why Chris was motivated to "drop out" of society. They are both strong willed characters, and Chris obviously felt wronged and betrayed when he leanred the true reason why his father and mother's marriage ended.
While his relationship with his mother is better, and we get the sense that Chris felt sorry for her on some level, he can't seem to forgive her, and along with his sense of wanderlust and adventure, along with his transcendentalist idealism, this drives him west and north, as far from that betrayal as possible.
What complicates the story further is that, while the relationship between Walt and Chris was mostly destroyed, Walt obviously loved his son, and said so openly. That's part of what makes this such a tragedy.