The boys applied paint on their faces in order to blend in with their environment and enhance their success at catching prey. It should be noted that they did not immediately paint their faces and establish their roles as hunters when they met on the island, but this occurred as a gradual learning process. Earlier in the story, Ralph, who later on assumed leadership of the hunting group, was unable to kill the prey he first encountered. He however continued to hunt and developed his skills, his will to survive and the need to provide food and security for his community, together with those who joined him.
The issue of the "beast" among the younger school boys also facilitated these changes. Ralph together with his hunters embraced savage characteristics in order to instill a sense of security for the young ones. Fear of the imaginary beast symbolized their primal instincts and their inclination towards savagery. Basically, by painting their faces and spears and calling themselves “hunters”, the school boys were adapting to their environment and evolving into a formidable force capable of protecting and providing for themselves.
In the novel Lord of the Flies Golding does several things to further develop the theme of human nature.
The boys put on paint and arm themselves with spears because it makes them feel stronger and superior to how they used to be. By giving in to their natural instincts they become more akin to savages as it makes them feel stronger. They feel empowered by the title of hunter. It makes them feel like they are in power and that everyone else is below them or prey.
On the surface the boys only do this because they want to. However, on a deeper level they do these things because it is in their human nature to act savage and assert their dominance.