The symbolism of the shelters derives to a large extent from their source, namely Piggy. Because he wears glasses and is the most intellectual among the boys, Piggy is often considered the representative for science and the civilizing influence of it. As such, he suggests that they ought to build shelters because it might be some time before they are rescued.
But the boys quickly reject the demands of building and keeping up the shelters and they end up rather forlorn and ineffective. The boys' inability to construct and maintain them suggests that they are incapable of re-constructing society in a way they understand it on the island. Their fear is too great for them to revert to the ordered and safe manner of living prior to their being stranded on the island.