Because they're paying for their Internet connection. It's not up to AT&T, Comcast, Verizon, or anyone else to tell me whether or not I should be able to go to Amazon's website or the local bookstore down the street's website. Amazon is paying for a bigger pipe, bigger servers, etc. Their website is already going to be faster/more responsive, sure. And IIRC I've seen local commercials in the OTA broadcasts of the Superbowl (probably because the Network has a deal set up with their affiliates across the country). Allowing Amazon to pay ISPs to "prioritize" their packets (or really to de-prioritize their competition) would be kinda like saying Wal-mart paying affiliates to not air competitor's ads (or I guess really delaying the broadcast of those ads to later time). -- Worst analogy ever.
ISPs are basically trying to get a bite of the apple from you and the site you're visiting. You've both paid for your connection, there are peering agreements so it doesn't cost them any extra for you to visit Amazon or the local bookstore's site, yet they want the local bookstore to pay extra to every ISP to keep their packets flowing to anyone equally. And as much as I'm sure you would pay extra to have your packets get priority, good luck winning a money battle with Amazon on who gets higher priority with your customer's ISP.