This is a noteworthy excerpt from that above linked page on pepto.de. I'm not sure how long that bit at the bottom has been there - the email from Robert 'Bob' Yannes.
Notice he says, this,
"I'm afraid that not nearly as much effort went into the color selection as you think. Since we had total control over hue, saturation and luminance, we picked colors that we liked. In order to save space on the chip, though, many of the colors were simply the opposite side of the color wheel from ones that we picked. This allowed us to reuse the existing resistor values, rather than having a completely unique set for each color."
The C64 palette toted as being the best severely limited palette of it's time, and it's certainly adored even now. According to that excerpt, the colors were chosen rather haphazardly, and not with complicated color theory principles in mind. Sounds like hardware geeks picked the colors out based on their preference at the time, hehe. Oh well, it works.