I would first consider Long John Silver as a father figure to Jim. I know, it seems like a paradox. At times, Silver shows extreme kindness and a paternal liking for the young narrator. At other times, however, Silver, although deformed like Pew, shows extreme brutality and cruelness in killing other sailors. With Silver, however, there is a constant softness towards Jim that transcends his dastardly pirate nature.
Dr. Livesey can be considered another father figure to Jim. As he becomes involved in the treasure hunt, he also shows consideration and kindness to Jim, thus, becoming one of many surrogate parental figures to Jim in the course of the novel.