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Please DO NOT listen to this guy. This auto-focus to the search box misfeature absolutely ruins any page viewing navigation. For people who use up/down arrow or pgup/pgdown keys to scroll down the page (which is pretty much all laptop users), this focus stealing misfeature would frustrate them to no end. I won't go back to any site that does this.
Is it still a misfeature on pages that fit on one screen, e.g. google.com, or (my own company's) mixrank.com? Isn't a better strategy to optimize for the common use-case?
I don't think it makes sense on Amazon. A typical amazon user may browse around and explore outside of search. Maybe most of the time they will search, but there are no doubt other use cases like using the fancy nav. It's even possible that they want to encourage user's the browse around a bit instead of finding what they want and leaving right away.