I bet apps and any electronics ship with Android are the one making the money. In fact, I think the hardware piece is the one making money.
Last time I checked, most Android hardware manufacturers - including Samsung (although that may be for other reasons) - were bleeding money. HTC's financial trouble are well known, Sony's Android division isn't profitable either.
Can you think of a single Android manufacturer that is raking it in?
Google also doesn't make the phones directly - other manufacturers like LG do. Can you think of any reason they would be making more money? Keep in mind that Nexus phones don't sell anywhere near the same quantity as widely advertised phones, like say, the Samsung Galaxy range.
Also, the apps that ship on Android are free...