They don't use it because they like Google Checkout or they want to promote it, but eBay probably felt their AdWords ads would be less competitive if they don't use it. And, besides, Buy.com has the funny logo. eBay continues to have meaningless ads that use templates. If you search for [ebay buy.com] on Google, the first result has this description:
Buy Buy.com, Vintage Sports Memorabilia items on eBay.
Everything for sale on eBay