Despite Ralph's best intentions and his maturity and integrity, his claim to being the leader of the island is challenged by Jack and his crew of boy-hunters. Here are a few quotes that support this notion and illustrate Ralph's lack of leadership skill.
Jack started to protest, but the clamor changed from the general wish for a chief to an election by acclaim of Ralph himself. None of the boys could have found good reason for this; what intelligence had been shown was traceable to Piggy while the most obvious leader was Jack (chapter 1).
In chapter 1, the narrator simply states that Jack possesses a natural flair for leadership that Ralph lacks. Ralph has asserted himself as leader, and though he does have important qualities that enable him to be a reliable chief, the fact remains that "the most obvious leader was Jack."
Later, in chapter 2, Ralph attempts to lead a meeting of the boys, but the narrator points out to the reader that being in a position of leadership does not come naturally to Ralph. He finds the experience destabilizing and uncomfortable, and he lacks confidence in his own ability to lead. According to the quotes below, Ralph is easily distracted and loses focus when he attempts to lead, and surely his uncertainty is observable by the others, which compromises his leadership role even more.
Ralph lifted the cream and pink shell to his knees and a sudden breeze scattered light over the platform. He was uncertain whether to stand up or remain sitting (chapter 2).
The passionate noise of agreement from the assembly hit him like a wave and he lost his thread (chapter 2).
In chapter 4, the boys in charge of the fire abandon their post at the wrong time. A ship passes by the island just as the smoke from the fire disappears, which means that an opportunity to be discovered and rescued has passed. Ralph's frustration with Jack, who has led the other boys away on a hunting mission, is intense, and at first, Jack is too ashamed of himself to do anything but avoid eye contact; eventually, however, he apologizes in front of everyone witnessing the confrontation:
The buzz from the hunters was one of admiration at this handsome behavior. Clearly they were of the opinion that Jack had done the decent thing, had put himself in the right by his generous apology and Ralph, obscurely, in the wrong (chapter 4).
Thanks to Jack's natural leadership skill, his apology is given more weight than perhaps it deserves. Ralph's tendency to get flustered interferes with the gravity of this situation, distracting the other boys from the fact of Jack's irresponsibility.
The possession of leadership skills does not guarantee that the leader will lead others to positive action; in fact, the opposite holds true in The Lord of the Flies. Though Ralph is better able to hold on to his civilized nature than Jack, the boys are drawn to Jack's character, and they follow him when they descend into the darkness of their own primal desires.