Because it looks different enough from the Brawl model(which was a straight rip from Twilight Princess) that it seemed to clearly be a different model. Especially in the E3 trailer, he looks WAY diferent than his Brawl/TP model. The biggest difference was the hair. In TP, Link's hair was kind of a brown-blonde color, and was clearly divided in to different "chunks." This was most likely due the the limited power of the Wii/Gamecube, but still, as in the E3 trailer, Link's hair was a bit darker brown, and had emphasis on individual strands, as well as having much longer/poofier bangs in front of his eyes. As more and more screens of him released, it became clear that it was in fact based on the TP model, but much better looking thank's to the power of the Wii U. It's also why his 3DS model seems to be an exact replica of Brawl's model, just with a lower poly count. His hair still looks a bit different than before, making me(and others) think that it may actually be his design in the unannounced Zelda U, which may or may not be a sequel to TP, much like Majora's Mask was, or Phantom Hourglass.
TL;DR: He looks a bit different, so we thought he was different. But that was a long time ago, and most of us have accepted that we were wrong.