I don't think its really all that overrated. Its a good game, and a lot of fans of the series as well as general gamers realize how good it is. Compared to the other Zelda titles, it is superior in many ways, but the other titles are all different to me. Each Zelda game has its own special significance and feel to it in my view. And yes, ten years later, this game still is quite good. There's a lot of crap thats released today too quickly, and we get a shell of a game when we were hoping for the whole deal.
When I think of overrated games, I think of things like Halo, and in no way do I feel that people obsessing over Halo is anything like someone thinking OoT is the best game ever. People liked Halo because of the online play, which is always good, but it dosen't make an entire game great. The story mode of a game is what makes the game, and OoT did itself justice without any addition online or multiplaying add ons for replay value. True, online wasn't even created for home gaming systems during OoT's time, but multiplayer was a big part of gaming during this generation.
Nintendo also seems to have a small reputation for making harder versions of games. As far back as Super Mario Bros., in fact, and the original Zelda as well, both had harder quests to undergo once the game was completed. This is sorta how I view Master Quest. It was a more challenging version of OoT, not just something created to milk the game for everything it was worth. They have done enough of that just releasing it over and over (N64 Collector's Edition, gray cartridge, game of the year edition, OoT/Master Quest CD, Zelda Collector's Edition Disc, Virtual Console). But hey, if people will buy it, why not sell it?