I think you are taking these quotes out of context. Charles Stross (http://en.wikipedia.org/wiki/Charles_Stross) is a writer and the books he is linking to are written by him. He uses the affiliate fees (maybe $250 a year) to help defray the hosting costs of his blog. The affiliate fee issue is only of a small part of his argument against Amazon's business model.
Personally, I think that $9.99 is a fair price to pay for a DRM-encumbered ebook. There should be enough in that amount to pay the author, the publisher, and the retailer, especially given that they should get a larger volume with the lower price-point. Unfortunately, it looks like the allocations between the three parties are way out of wack.
Some data. Here's Amazon's US & UK affiliate compensation charts. In the US, 10% on Kindle purchases, one of their higher payouts. I assume the UK program will offer specific Kindle payouts soon now that the Kindle is going international.
And because I was downmodded for that, here it is...
> So, to summarize: what have I got against Amazon's Kindle?
1) DRM. (It's unethical, immoral, fattening, and a royal pain in the ass. To be fair: this also goes for other ebook platforms.)
2) Amazon reserves the right to delete work from your Kindle. (Under circumstances which are now a little clearer and a little tighter, but nevertheless still present.)
3) Censorship.
4) They're using their monopsony position to fuck over their suppliers (i.e. the publishers) in a manner that threatens a catastrophic crash in author royalties in the medium term (up to 5 years). NB: as a reader, you may enjoy the short term price benefit, but you'll pay for it in the long term in reduction of choice.
5) Their actions may start a trans-Atlantic price war between publishers, to the detriment of authors (again, in the medium term).
"I don't link to Kindle ebooks because Amazon don't pay an affiliate fee on them."
Riiiiight.