How the heck does Amazon make money?

I was on Fatwallet a couple days ago and noticed that they had a 128 meg compact flash card for $4 after a $15 rebate. I needed to get my total above $25 so that I could get free super saver shipping. They had some gillete razors for free after rebate, so I added them. That brought my total within 7 cents of the $25 necessary for free shipping. I then checked EveryDeal, which lists every item on Amazon by price. The second lowest price was a package of Vicks cough drops for 68 cents. Added that to my cart and checked out.

I got an email the next day from Amazon that part of my item had shipped... just the cough drops. I have my packages shipped to work because I'm never home when delivery people come by, and if packages get left on my door my neighbors will steal them. When I got to work, there was a package waiting for me - a small cardboard box, about 2 inches long and an an inch and a half high. Opened it up, it contained a packing slip, two plastic air pillows, and a small box of cough drops - the kind you buy at the checkout section of the grocery store.

Does Amazon really have their shipping costs so low that they can make money mailing me a box of cough drops - especially with that much packing? I thought that the logic of super saver saver shipping was that stuff would get bundled together when they ship it - but shipping it individually seems to defeat the purpose.