According to Shuttleworth, the Amazon results are not advertisements. They’re simply things that match your search terms. Search for “iPod” and Unity will find any iPod manager apps you might have installed and it may also return some results to buy an Apple iPod from Amazon. If you click through and end up buying a new iPod case or something of the like, Canonical gets a small kickback.
It seems pretty harmless, but it is very different. I’m not aware of another operating system that integrates shopping results at such a low level. Apps yes, OSes no. As with all things radically new, it rubs some people the wrong way – just look at this hilarious bug report. Combine that with the fact that Amazon isn’t a terribly useful first choice for web-based results and you have a perfect little storm for your Ubuntu teacup.