Hi everyone,
First of all, a disclosure: I'm the CEO of Smashing Magazine, a leading online magazine for web designers and developers.
Here's my opinion on Affiliate Links:
Affiliate ads are a kind of paid content, and paid content is a betrayal to the reader. It's a hidden advertisement, and the Adblock Plus (and our) guidelines require that all advertisements are marked as such.
If someone posts an affiliate link, she will in most cases mention a product or service she otherwise wouldn't have mentioned. She wants to make money through advertising for others without admitting it.
Mixing up content and advertising without acknowledging the readers is wrong. I'm strongly against whitelisting affiliate links.
To go further, paid content shouldn't be the future of the web. Many publishers feel forced to go this way because of Adblockers, but I think that is so wrong!
Markus