I really tried AA on a few of my sites, and eventually gave up and switched back to Adsense. I even created a custom ad system which tried different Amazon products, tracked impressions and clicks, which gave me the data on which ads were more likely to be clicked on. I went up from the initial 0.5% CTR to 5% CTR, which I felt really proud of. But then you have to realize that once these people land on Amazon, they have to convert again in order for you to get paid, and the conversion rate is like 1-2%.
So you end up with shit like this: 250 clicks, 4 items ordered, $2.40 earned (straight from the earning report).
Now think how much Adsense would pay you for 250 clicks. I average $0.432 per click (just checked). So $108 is what I'd expect to earn with Google. That's 45 times more than Amazon.