There are several problems with it:
1. the certificate is not generated by you (in the Free or the Pro plan) but by them and these certificates are for multiple domain names. So you end up sharing your certificate with other domains / websites of dubious nature that are also on CloudFlare's network.
2. CloudFlare only secures the connection between users and the CloudFlare network. It does not secure the connection between CloudFlare and your hosting service, unless your hosting service also supports TLS/SSL connections and you activate their Strict SSL option.
For the purposes of hosting a project website, secure connections are more important than ever due to the potential of external attackers, which could very well be a government institution, to infect distributed binaries or source code. Instances like XcodeGhost will become more common imho. And a secure connection between your user's browser and your hosting server is not 100% secure, but it's a good start. And towards that purpose CloudFlare Free in front of GitHub Pages isn't very good ;-)