Zeus doesn't so much punish the Phaeacians as he allows Poseidon to punish them for aiding a man the Earthshaker had a legit beef with. Turning their better-than-everyone-else's sailing ships into rocks, effectively taking away the gift of the sea, is something that would fall under Poseidon's dominion rather than his brother. And the stone boat thing is a compromise between the two, when Poseidon being who he is probably wanted to do something involving earthquakes and tidal waves, and Zeus talking him down.
Added: Poseidon is also the Phaeacians' patron god, so this is him taking some or all of that away, which is probably seen as his right. His punishment also fulfills an earlier prophecy, which probably also influences Zeus's actions.
Added: Poseidon is also the Phaeacians' patron god, so this is him taking some or all of that away, which is probably seen as his right. His punishment also fulfills an earlier prophecy, which probably also influences Zeus's actions.
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