Well, it’s never specified why they chose Threepio specifically. Although the Empire didn’t exactly treat them very nicely, so I don’t see why they’d worship them. It was probably because of the Empire that the Ewoks were initially planning to kill Luke, Han and Chewie. Leia was the exception as she’d previously saved Wicket from a stormtrooper. (Also I don’t see why they’d worship the giant death machines that trample their forests.)

Also as Frink already pointed out, Threepio does stand out being golden.
(Which is the specific explanation the EU gave; http://starwars.wikia.com/wiki/Golden_One.)