In Lord of the Flies there can be found several themes. I will give you the theme according to Golding, my teacher and me.
"The theme is an attempt to trace the defects of society back to the defects of human nature. The moral is that the shape of a society must depend on the ethical nature of the individual and not on any political system however apparently logical or respectable. The whole book is symbolic in nature except the rescue in the end where adult life appears, dignified and capable, but in reality enmeshed in the same evil as the symbolic life of the children on the island. The officer, having interrupted a man-hunt, prepares to take the children off the island in a cruiser which will presently be hunting its enemy in the same implacable way. And who will rescue the adult and his cruiser?"--William Golding
The defects or flaws within man cause the defects or flaws within society.
Man in a civilized society is no better than children running wild outside adult supervision.