The Enotes guide to literary terms defines an allegory as "an extended metaphor in which a person, abstract idea, or event stands for itself and for something else. It usually involves moral or spiritual concepts which are more significant than the actual narrative" (source). Lord of the Flies is an allegory about human nature and the two principle drives that inform most of our actions and choices. What the Lord of the Flies is is a society in miniature--a microcosm which represents the larger world and what happens in it. In real life, in real human societies there will always be the spiritual "Simons", the rational leaders like Ralph, the aggressive hunt-hungry Jacks, the awkward intellectual Piggys, islands, bullying, dog-eat-dog mentalities, and the survival of the fittest mentalities. Sure, Golding chose a bunch of British school boys, but it might just as easily have been young ladies, adults, etc. Look at "Survivor," look at "Lost"--these television shows still carry with them elements of Golding's novel. The final message, possibly, might say something about how we have to stick together to survive, how we have to protect the weak, how we must recognize that there is a darkness that potentially resides in each of us, but we must learn to control it for the greater good of society or we will all be lost, or all degenerate into bloodthirsty warriors. See the themes for more of what Golding is trying to teach us.
The novel "Lord of the Flies" can certainly be considered an allegory. Each character represents a different part of human nature. Simon is the best in all of us. He could be considered the "Christ like " figure. Ralph is our reason and Jack is our animalistic side. The head of a pig on the stake is even referenced as the devil. According to Enotes references to literary terms an allegory is
"an extended metaphor in which a person, abstract idea, or event stands for itself and for something else. It usually involves moral or spiritual concepts which are more significant than the actual narrative."
Keeping this in mind we can easily see that the concepts and details in this novel create the allegory. Being familar with Golding's philosophy also aids in the understanding of the underlying meanings. Golding is trying to say that mankind, when left to his own devices will become animalistic to survive. Each human being has a dark side and an ability to return to our basic roots when threatened.
The links below will provide a great deal of valuable information on this novel.