Lord of the Flies is a symbolic novel, and each of the boys is representative of some aspect of the human experience. Ralph is the physical, Piggy is the intellectual, Jack is the inherent sin nature. That leaves Simon, the one who represents the soul/spirit/conscience. Because of that, Simon is especially sensitive to the things happening below the surface. He's aware of the spirit world, the world in which our true selves are revealed. That's why he knows the beast is us, the beast is within--not something which can be fought or killed with weapons.
In Lord of the Flies, Simon represents the Christlike character; therefore, he is blessed with insight and understanding beyond any of the other boys. Simon doubts the existence of the beast because he recognizes that the beast is within each of the boys and that it's not a separate entity that is going to attack them.