I loathe online store sites that auto-focus the search box. Worst are the ones that do it on every single page, including item detail pages. I use the space bar to scroll webpages down, especially on my laptop, which has a very small screen so that I almost always have to scroll down to get past header crap and get to the meat of the page. And no mouse, just a mediocre touchpad.
I can maybe accept auto-focusing search on the homepage, but there is no excuse for an item detail page. Even if I got here through a search engine, I probably want to see if this item is the item I wanted before I go searching the rest of your store, and that's going to require scrolling.
Definitely make the search box the first input in the tab-order though. Then if I do want to go straight to search, I can tap tab and then start typing. Otherwise, I usually want to scroll first and nothing is more frustrating than nothing happening when you hit space, only to realize that some tiny obscure search input buried in the corner of the page header that you didn't even realize was there is filled with spaces.
/less ranty
The best of both worlds would be to only auto-focus the search input if the user starts typing letters, and ignore space/arrow keys. We do this on Grooveshark actually.