One significant theme in Into the Wild is the deep and secret alienation that Chris felt for his parents. He was very angry at him, although his complaints are clear. The reader knows he's angry, but isn't sure why. We see from this relationship the different standard of morals that Chris had for his family and his friends. He was much more lenient towards his friends, forgiving them for things which he would never forgive his father for.
Another theme was Chris' desire for exploration and explanation. Chris wanted to travel because he wanted to find out about mankind. However, so stubborn was Chris that he did things his way, and didn't listen to the preparations he was told to undertake. Chris had a problem taking advice, either from the experts or his friends/family.