I believe that you are correct. Charlie Fox initially has respect and devotion to his father. As a boy he recognizes that his father is unique but those characteristics are interesting and Charlie does not see them as being dangerous.
As their journey becomes harder for him and his mother, he begins to recognize that his father has problems. He loses his respect for his father and begins to develop fear and anger towards his father. The book takes the reader on the journey of him sharing the story of his unusual father and life, but in the end it is still a young man's journey towards adulthood.