Man, when perfected is the best of animals, but when separated from law and justice, he is the worst.
In Chapter Four, the sadistic Roger restrains his arm from throwing the stone, "that token of preposterous time," from hitting little Henry on the shore. Golding writes,
Here, invisible yet strong, was the taboo of the old life. Round the squatting child was the protection of parents and school and policemen and the law. Roger's arm was conditioned by a civilization that knew nothing of him and was in ruins.
William Golding's allegory clearly points to the inherent evil in man unrestrained by society, "unperfected."
To keep it simple, I believe the primary question Golding asks, and answers to an extent, is "Are human beings inherently evil or savage?" I agree, however, that there are many sub-questions, such as: "When outside of civilization's rule, how do people act?"
It definitely answers the question about whether or not a group of "civilized" British boys would succumb to the darkness of man's heart and allow that to color their existence on an isolated island where there is no adult supervision to keep them in line.
Almost immediately, they shed the clothing that makes them look civilized. There is also a breakdown in communication and between what the boys need to do for survival and rescue and what they want to do without adults around. This division is clearly defined by Ralph, the sensible one, and Jack, the one who wants to spend all his time hunting and swimming...doing just enough to eat and enjoy life, but not enough to live well as a group until rescue comes along.
The end result is a quarrel for "troops," for living quarters, and for tools (Piggy's glasses). Jack realizes that his world will not be allowed to exist as he wants it as long as logic (Ralph), knowledge (Piggy), and innocence (Simon) survive. Therefore, he allows the dark side of his nature to overcome and they are murdered.
Jack is the only one who does not believe in the inevitability of rescue. Ironically, it is his own fire which brings the rescue that Ralph so desperately needs.
So, the answer is: The boys are not so innocent, nor are they so civilized. Anyone, anywhere, can and will descend into darkness if put into a similar situation.
"Lord of the Flies" was written after World War II when many were questioning how such evil events like the Holocaust could have happened. Golding suggests that in the absence of competent, moral leadership people will gravitate to cruelty and depravity. There is a "dark side" to humanity that must be controlled by the rules and consequences of a strong government. Thus, the reason for the holocaust and other crimes against humanity was the void left in German leadership after World War I. This allowed men like Hitler, or Jack, to come to power.
I'm not sure we can ever really say a book answers any one single question - particularly when written by a Nobel Prize-winning author like William Golding. "Lord of the Flies". The novel deals with a whole host of themes: the "darkness of man's heart", the potential that evil is an quality innate in humans, what it means to be a child and to grow up, the interaction of humans with nature... and so on. There are plenty of questions asked, but not many answers.
If you think of the novel as treating on the human condition, you might think of it - in the very simplest terms - as posing the following question: what happens when a group of young boys are unsupervised on a tropical island?
And, of course, from there, you might ask the question any good student would ask of a work of literature: is this believable? Do you really believe that, within the same situation that novel sets up, the same things would happen?