In order to look at Lord of the Flies as political allegory, particularly if one is to focus on the role of Simon as the religious representation, one must consider his inability to influence the politics of the island as an important part of that allegory.
As Simon is the only one who realizes what the boys really fear, and the only one who recognizes how to overcome it, he stands alone amidst a crowd that is unable to see the real problems, one that is always getting caught up in the superficial and trying to fix symptoms rather than treating the disease.
Without trying to argue that religion can solve the world's problems, it is easier to suggest that it does provide a powerful perspective on what is important and a framework for looking at what is right and wrong, etc. Simon sees that the beast is within the boys and he sees it because of his willingness to acknowledge and listen to the beast, the supernatural.
But the political world cannot allow for the influence of the supernatural just as the boys cannot accept Simon and so they must destroy him or refuse to allow his perspective to influence their decisions.