The Lord of the Flies is certainly a coming of age story, even though it occurs within a very limited time frame, and doesn’t follow the boys into adulthood. A coming of age theme is usually present in a text through several markers:
A loss of innocence: this is seen clearly when the boys lose their humanity in a tribal dance, and in their hysteria, murder one of their own. The death of Simon marks a significant turning point in the novel, since it’s the first death that occurs at the hands of other boys, rather than as an accident or a result of the crash.
Questioning authority: Many of boys question Ralph’s authority, though Ralph was almost unanimously elected at the start of the novel. Though they frequently wonder what grown-ups would do in their situation, most of the boys reject any attempt at structure in order to spend their time hunting instead.
Rebelling against society: The loose society they set up for themselves is quickly dismantled by Jack’s insubordination and subsequent tribal takeover.
And finally, if you want to get really depressing, Ralph especially experiences the truly adult acceptance of one’s futility to change society in meaningful ways. (This is an admittedly nihilistic read of the text.) He can’t turn the tide back to his authority, can’t convince the boys that there is no beast, and can’t save his friend Piggy. In the end, the Captain that rescues them is like a disappointed father, scolding children. While the boys came of age and lost their humanity, in the end, they are still little boys.