In my understanding, affiliate links' value are demoted. I think it's pretty easy for google to see a link is an affiliate link. Clicking it will add a certain type of cookie and I believe Google can easily distinguish between these links. Adding a reL=nofollow to the link is the appropriate way to have these links on your site. Beside that, Amazon's affiliate programme is well known, so Google will definetly compensate for that.
However, people aren't convinced that the rel=nofollow attribute doesn't give any value to the link. Some believe it still adds to domain diversity and other fankers besides the "plain" link juice.