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What is the allegory of Lord of the Flies?

The island itself is an allegory for society. The author shows that, like children stranded on a deserted island, society can break down due to bad leadership, mob mentality, and a lack of true civilization.

James Stern of the New York Times said that the Lord of the Flies is:

an allegory on human society today, the novel’s primary implication being that what we have come to call civilization is, at best, not more than skin-deep

The main allegory for Lord of the Flies is that without civilization, savegery takes over.  The Lord of the Flies and the Beast are not realy physicall characters.  It is the evil that is in every human being.  Without civilization the boys unleashed this evil.  Piggy stood for intellect which every civilization needs, when he died it showed that savegery had completly taken over.  Also Simon stood for morality, but not because civilization told him to be moral, but because he knew that morality was natural.  But this book shows the allegory that savegery is stronger and more natural than civilization, this it took over. 

The death of Simon indicates how morality and goodness cannot survive within savagery.

Notice that this savegery stops when the navel man appears.  he also stands for civilization and it has come back, so savegery is put away. 

srry if my grammer is bad...=)

The name “Beelzebub” can be traced back to the Old Testament. In
II Kings 1:2-16 (King James Version), the god of the Philistine city of
Ekron is given the name “Baal-zebub,” meaning “Lord of Flies” in Hebrew.
In post-Biblical Hebrew, the name became transformed to
“Beelzebul,” which can be construed as “Lord of Dung” (Gaster 374).
This connotation, along with the name’s etymological association with
flies, probably accounts for the fact that in certain Jewish religious texts
the fly is considered an impure creature symbolic of corruption and evil.
The Berakhot of the Talmud, for example, states, “The evil spirit lies
like a fly at the door of the human heart.”

This somewhat lengthy quote is taken from a commentary on "In the Lake of the Woods" (Tim O'Brien).  It provides a good link between the two books.  In Lake, the flies are evil/Satan, always there during the Mai Lai experience in Vietnam; they are the presence of Satan.  In "The Lord of the Flies" we see Satan himself at work in the hearts of what we might have thought to be the "innocents."  Much like snakes, flies always seem to have some kind of "uncomfortable" if not outwardly evil about them; perhaps the fly's attraction to garbage, and it's unwillingness to leave us alone despite our best efforts makes it a great reminder of our tendency toward evil.

You might want to read the entire article referenced below.