Given that the DDoS wasn't targeted at "https://github.com/" but rather "https://github.com/greatfire/" and "https://github.com/cn-nytimes/", two projects that can reasonably be described as not being pro Chinese government, it seems that github was targeted for hosting anti-Chinese 'propaganda'.

Thanks for the clarification!

There is the Github you see and use, then there is the Github you don't see. It's a service that allows files/information to be uploaded, downloaded, shared, by pretty much anyone. That's something some governments sadly don't like.

Note that it seems to be attacking two specific projects, according to the details above, one of which is to get around the restrictions of the Great Firewall of China. It's most likely an threat about the advisability of hosting something unapproved-of.

Interestingly enough they have succeeded in pulling those projects down.