"Probably the biggest reason is that nerds don't make any attempt to fit in" is very similar to what Graham writes, and is actually compatible with it:

The main reason nerds are unpopular is that they have other things to think about. Their attention is drawn to books or the natural world, not fashions and parties. They're like someone trying to play soccer while balancing a glass of water on his head. Other players who can focus their whole attention on the game beat them effortlessly, and wonder why they seem so incapable.

Even if nerds cared as much as other kids about popularity, being popular would be more work for them. The popular kids learned to be popular, and to want to be popular, the same way the nerds learned to be smart, and to want to be smart: from their parents. While the nerds were being trained to get the right answers, the popular kids were being trained to please.