In many ways Simon is the most interesting character in the story. He is a very spiritual boy and the only boy that intuits what is good. He is also very in tune with nature. He is also a boy of great courage and faith. For instance, he is the only boy who is not scared of the beast. He even suggests that perhaps the beast is only a figment of their imagination. The most famous quote of the book arguably is his words, "What I mean is . . . maybe it’s only us."
In light of all these points, when Simon says to Ralph that all will be well, there is a spiritual quality. There is unwavering faith that in the end that everything will be alright. In other words, there is an inner peace about Simon that things will work out in the end. The irony, of course, is that it does work out for Ralph (not without hardships), but Simon dies in the process.