Rocks symbolize primitive human instincts and destruction. Jack's power base is located on Castle Rock. Throughout the novel, the boys roll rocks down the mountain and hills to witness the awesome destruction they cause. Roger rolls a large boulder towards Piggy, which ends up killing him. While Ralph is hiding in the brush, the savages roll a massive boulder that forces him to leave his hiding place. Rocks are used as weapons and cause destruction throughout the novel. The earliest humans used rocks as tools and weapons to survive. Jack and his band of savages parallel these Neolithic humans by rejecting civilization and embracing primitive human instincts. Much like Jack's band of savages, rocks are callous, sharp, and dangerous. Golding associates the destructive nature of rocks with Jack's tribe throughout the novel.
Shelters symbolize civilization and protection throughout the novel. Ralph and Simon work on the shelters alone after the rest of the boys leave to bathe, play, eat, and hunt on the island. Ralph and Simon share an affinity for civilization, structure, and morality. The shelters are built to house and protect the littluns from not only the forces of nature but also the "beast." Jack, who represents anarchy and primitive human nature, dismisses the importance of shelters and refuses to help build them. The fact that the shelters become progressively unstable and shaky foreshadows the boys descent into barbarism on the island. The shelters represent the degree in which civilization diminishes throughout the novel.
In Lord of the Flies the shelters represent civilization, safety, and security from the elements and the beastie. When Ralph tries to get everyone to build a sturdy shelter, he is trying to "build" an island civilization and keep all the little 'uns safe. Jack is not worried about building shelter. Jack is worried about meat and the thrill of the hunt. Symbolically, he is against what Ralph deems important and vital to survival.
The rocks are mostly weapons and they represent Jack's tribe of warriors and outlaws. Roger first uses rocks by throwing them at a little 'un and trying to scare him and bully him. It is also a rock which kills poor Piggy. Rocks are also what and where the warriors make their home on.
As mentioned in other responses here, shelters represent civilization and rocks represent savagery. The shelters are associated with Ralph—he is the one who spends the most time, assisted by Simon, constructing the shelters. He is angry that few of the other boys care about the shelters; in fact, the quality of the last shelter they put up is questionable because they didn't have enough people to help. This shows that it is impossible for a few dedicated people to create a strong society if most people won't do their parts.
Rocks are most often associated with Roger and Jack, the two boys who most represent the descent into savagery. Roger throws rocks toward Henry in chapter 4, yet observes a "taboo of the old life" and aims to just miss him. When the boys engage in their savage dance in chapter 9, it takes place at "the open space of rock beyond the fire." When the boys begin to attack Simon, he "fell over the steep edge of the rock" onto the sand, and the boys "poured down the rock" after him to murder him. After that night, Jack moves his tribe to Castle Rock where the boys set up a defense system with a log and a large boulder. When Ralph and Piggy call on them there, Roger zings stones at them, very close to Ralph's head, and ultimately murders Piggy with the boulder.
Another way of looking at the shelters and rocks which parallels the ideas already mentioned is that the shelters represent altruism and rocks represent selfishness. When Ralph wants to build shelters, he is thinking of the good of the others, particularly the littluns, and he gives up his own time that he could have spent playing and indulging his own desires in order to serve others. When Roger throws rocks, he is obviously not considering the harm he is doing to others; he does it because it gives him a sense of power and control. Jack makes his tribe camp on Castle Rock even though Ralph had previously pointed out that it was a difficult place to live because it lacked easy access to water; Jack makes life harder for the other boys just to satisfy his own belief that Castle Rock "would make a wizard fort."
Golding uses the shelters to represent not just civilization, but also altruistic behavior, and rocks to represent not just descent into savagery, but also selfish actions and attitudes.