The last seems to be the correct answer - affiliate links are used. I see no evidence Stallman is incorrect and the Shuttleworth blog article does not say they don't use affiliate links.
http://askubuntu.com/questions/192725/how-do-i-make-sure-tha...
> The Amazon affiliate referral happens if you've arrived at the Amazon property via a 'tagged' link. Both links clicked via the dash which go to Amazon sites, and the shortcut in the launcher will add the tag. The tag adds a cookie which lasts for 24 hours. If you buy anything during that period, Canonical will get some affiliate revenue.