Mine felt higher when I first got it, but that was running 'naked'. I added a screen protector after a couple of days and could swear that the Home button still felt higher, but it's definitely flush with the screen protector now. So who knows if I was just imagining things or if the button has sunken in a bit.
Off topic, but I really wish Samsung had gone with a capacitive button rather than the physical one - I can already see the day coming when that thing quits altogether, just like the power button on my last phones. I try to avoid using it as much as possible for that very reason - if I could find an app to map that functionality to a screen press somewhere else I'd be doing that instead.
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