While there is no explicit reference to religion in William Golding's Lord of the Flies, there are many religious aspects to this story. In fact, in one sense the novel is a kind of religious allegory which is set in a figurative Garden of Eden.
The tropical island is a place which is free from evil at the beginning of the novel. It is a pristine place where the boys have the opportunity to create a kind of perfect world until they are rescued. Unfortunately, the boys are soon tormented by things the littluns refer to as "beasties," though it is clear they are the "snake-like" tendrils which are common in a tropical setting (like the snake in Eden).
Simon is the most obvious religious symbol, as he is the character who has a spiritual sense of what is wrong with this island--it is the heart of man. He is killed while trying to speak the truth to them. As his body floats out to sea, the imagery is of a saint who has a halo glowing around his head.
The water rose farther and dressed Simon’s coarse hair with brightness. The line of his cheek silvered and the turn of his shoulder became sculptured marble. The strange attendant creatures, with their ﬁery eyes and trailing vapors, busied themselves round his head.
On another level, this is a novel full of pagan rituals, such as the pig hunts and the sacrifice of the pig's head known as Lord of the Flies (another name for Beelzebub, or Satan). The only real "god" (with a lower-case "G") in the novel is Jack presiding over his tribe of savages.
It is perhaps too much of a stretch to presume that Golding intended for this novel to be a purely religious story; however, he certainly included plenty of religious trappings and imagery.