They are used for reasons not clear. Originally there was the idea that people would reprogram the 16u2 to make other kinds of USB devices (like you can do natively on a micro/leo); this wasn't promoted or made easy, though, so there are only a few projects that do this, (hoodloader, unojoy, etc), and they're not widely used. If this had been promoted and supported better, this could have been really cool, but 99+% of them stay programmed as a usb serial adapter :-/
See the datasheet for an application schematic; You can also reverse engineer an el-cheapo serial adapter from ebay (I used both as resources when I rolled my own CH340G serial adapter).
Yes, 16u2 is a general purpose microcontroller, it must be programmed to act as a USB-serial adapter.