I like the previous answer, but I wanted to add a few of my own ideas. Simon is an interesting character in LOTF. He's sort of a "hippie type." What I mean by this is that appears to have a sense of "goodness" that is built into him on a programming level while the other boys have had their concepts of good and bad handed down to them by society and their parents. The longer that those boys are away from those influences the more their values deteriorate.
Simon is different. Notice the way in chapter three that he helps Ralph build his huts when no-one else is interested. Then, while walking through the woods, he helps some little kids reach a branch they are too small for. Simon seems to have an inner "goodness" that does not depend on adults or society to feed it.
He does appear to be driven into the woods by the general disharmony between Jack and Ralph, coupled with the failed attempt to finish the shelters. The cool part is that he finds a nice serene spot to settle down in. From his hideaway in the "bower" Simon is able to observe the beautiful world around him. He is in touch with nature and the natural environment. He has a keen sense of human nature that he can't express.
I think that he heads for the bower as a way to "level his waters." The disharmony of the boys and their squabbles has upset his natural sense of balance. By going to the "natural spot" he is in a way able to recharge and regain his composure.
Wile not directly stated, it is suggested that Simon goes into the jungle by himself in order to escape the ever-increasing tension between Ralph and Jack. When the two carry their argument down the beach, Simon follows them for a few steps, then stops. He sees a little mound where someone had attempted to build a house or hut, and his reaction is to frown. Did it remind him of the fight between Ralph and Jack? Does he see in it the slowly unraveling society of the island, and remember that they essentially have no shelter, no home? It's not clear, but after seeing this mound, Simon turns and walks into the jungle with "an air of purpose." So perhaps he simply needs to be alone for awhile.
Of course, once in the jungle, he finds his solitary thicket, where he will later discover the truth about the Lord of the Flies. So maybe some part of his unconscious knows that he can only be safe, and will only realize the truth, when he is separated from the madness building around the other boys.