Great question. The idea of a natural order applies to both the natural world and the world of human society. It even extends to the heavens, so that when comets or other uncommon sights appeared in the skies, they were taken as signs that a change was happening in the order of the world.
In this case, the storm is so intense that it essentially turns the ship over and throws the people on it out of the places they should be in (namely, on the boat). This relates to The Tempest because there was a social/political storm that upset things in Milan. The sailors are on the island because of the literal storm; Prospero SHOULD be back in Milan as Duke, but he's on the island because the political storm dumped him and Miranda there on the island. Literally or metaphorically, they're all shipwrecked by a storm.