I've never used kontera, so might be wrong on this, but my understanding is that it's pay-per-click advertising. OTOH, amazon is an affiliate program that pays a commission when someone buys something.
This is correct. Kontera is similar to Adsense. It took me two years to collect enough clicks, but I finally got up to $100 to get my commission payment from Kontera.
Personally, I find the pop up windows to be rather annoying, so I am removing them from my sites now.