Apple's site doesn't have to focus on discoverability. Compare for example, Apple's store section vs. their actual product pages - the former is a lot busier and "harder to navigate" than the latter. When you get into the business of selling a bunch of stuff in a discoverable way, your design needs change.
Keep in mind also that the Apple Store sucks at discoverability for non-Apple products - Apple does a marvellous job funnelling you towards the MacBooks and iPods, but a poor job exposing, say, third-party accessories. This works great for Apple, but would be instant death for a company whose entire bread and butter is selling third party goods.
Now consider that Apple has how many core products? What you see on the root store page is it. Everything Apple makes and sells is right there. Now compare with how many products Zappos is in charge of selling and you start seeing the scale difference.
You are comparing apples (no pun intended) and oranges.
Because according to Andrew, they make $1 billion in sales. The site is making a lot of money with the existing design. I can see why they don't want to fix what is not broken.
