Firstly, it wasn't until 2011 that YouTube settled the 2007 lawsuit to allow artists and publishers to enter into a licensing agreement with YouTube. This was after the "$12" quote was provided above.
As this article explains an artist/publisher has the following three options: keep the song there, take it down or make money off of it.
If the third option is chosen the song appears with the artist information and typically a link to iTunes. You can see an example of this here where a user has uploaded a version of Smashing Pumpkins "Disarm" and it has been marked as such.
However, if you look at the main RickRoll video from Youtube, the one with 64 million views, it isn't marked with artist information. However, the VEVO one does and so does another one that was added later.
So they have chosen not to make money from the original video. Thus the $12 is realistic, maybe the $12 wasn't even made from that version of the video. Considering the VEVO video now has over 50 million views and there are other videos marked as copyright, someone is making money from them. However, how much Rick gets directly from this is not currently public information.