The phrase "lord of the flies" is often associated with the mythological figure of Beelzelbub.
The name Beelzelbub, from the Hebrew, literally translates to mean "lord of the flies" and this figure is depicted in mythology as a demon in the form of a fly. More specifically, Beelzebub is a name used for "the devil" in some ancient Jewish and Christian texts (and the name is associated with the enemy god, Baal).
So, in addition to its meaning within the text, the title also references these ideas drawn from well-known mythology. One question then becomes, why would Golding title his novel with a reference to the devil?
According to scholars of Hebrew literature, the figure of the fly (and its associated god-figure) represents impurity and evil. Perhaps a more compelling view of the use of this reference in the novel's title is to see the idea of Beelzebub as a representative of animalistic, sanguine and brute impulses that stand counter to notions of restraint, civility and tolerance.
We might argue that this conceptual conflict animates the action of Golding's novel.
"Ralph’s reliance on reason and logic contrasts with Jack’s steady descent into savagery. They thematically represent opposite aspects of human behavior" (eNotes).
The impulse toward expressions of savagery is repeatedly indulged by Jack's character and those who eventually follow him. The symbol of this brute behavior is the boar's head, which "speaks" at one point.
"Fancy thinking the Beast was something you could hunt and kill!" said the head.
Considering everything above, we might ultimately suggest that the meaning of the title is a commentary on the inherent evil that exists in human kind. Civilization cannot eradicate evil impulses and savage tendencies but can only mask them or offer alternatives in controlled settings. Take away the controls and the mask falls away.