If you’re having trouble with a root domain on Github pages you may want to check out the Hosting product we (Firebase) just announced. It handles naked domains by having your root A record point to an Anycast IP that serves content from a global CDN. It’s lightning fast. We also support SSL (full SSL, not just SNI) and do the cert provisioning automatically for you.
Check it out: https://www.firebase.com/blog/2014-05-13-introducing-firebas...