I think Paul Graham is simply taking note of the problem without making any evaluations as to its cause: girls are largely turned off from programming by the time they're 13. The cause has been largely discussed here already: social bias.

These gender biases are not presented to our DD9 from her family, but she's constantly exposed to them nonetheless, and I'm constantly having to provide counter-messaging in response. I consider it a victory that DD recently decided it was okay to like blue. One question I get with some regularity which displays the insecurities she's getting from society regarding gender: "Dad, do you wish I'd been born a boy?"