A fear of the unknown runs throughout the novel. To begin with, the boys don't really know what happened at the start of the novel. They have only rumors and bits of stories about a war. No one knows where they are. Therefore, no one could rescue them even if the war allowed. When the boys first gather together, they can't really keep count of how many boys there are (they don't know). When they do get together, the things that move in the dark, such as the snake, are the sources of fear. What is it that makes the boys feel like something is watching them when they are hunting? What is it? They don't know, and it terrifies them.
To give more specific examples, consider the following. At times the mirage makes distance seem to change, and no one really knows why In chapter 5, Ralph speaks of things breaking up and says that he doesn't know why. When the parachutist comes to the island, the boys can't recognize him as human. They see him as "the beast" instead. Soon after, Ralph realizes how much he can't remember about what has happened, and that they are all changing. All of these things, and more, frighten the boys.