To me, the theme of this book is fairly clear -- Golding is saying that human beings are inherently evil. He is saying that people have a natural tendency to do evil that is stronger than their natural tendency to do good. The origin of evil is within human beings, he says.
The story that unfolds in the book shows these things -- Ralph (good) is nowhere near as strong in the long run as Jack (evil).
Golding is saying that human beings must have all the rules and institutions of civilization if they are to have any hope of behaving well.