Lord of the Flies has more than one "theme," or meaning, but the overall and most important one is that the conditions of life within society are closely related to the moral integrity of its individual members. In Golding's own words:
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?
In the novel, Golding seems to show the reader that this "ethical nature" is not inherent in mankind. Indeed, there is a certain capacity for evil that resides in man; his morality is simply superficial. Nonetheless, it is this moral integrity that must prevail in order for him to be ethical and thus for society to be maintained. Without this suppression society caves in upon itself (as seen in the book), lawlessness reins and life becomes a free-for-all.
Although this is the main idea of the story, others exist underneath it. The most prominent of these, probably, is the fact that often times people single out another person, or another group of people to look down upon in order to feel secure. Piggy's character personifies this societal flaw, as he is always shunned and made fun of.