GHP means you're subject to github's downtime, which tends towards more frequent than s3 (outside us-east-1). Worse, you can't run HTTPS with GHP and a custom domain.
You could use CloudFlare's flexible TLS, but it's unsecured from their system to your site, which has resulted in carrier level content being injected[0].
That's what got me to host my Jekyll sites on my own too (lack of proper end-to-end SSL on a custom domain).
Also, if you're not using S3 / CloudFront you can use Let's Encrypt to issue free SSL certificates on any cloud hosting provider.
It's an awesome set up once you know how to get everything up and running.
I even recently released a course[0] that explains how to do it step by step (setting up a custom domain, hosting multiple sites on 1 DigitalOcean server, A+ SSL ratings for both nginx and Apache, etc.).
It takes less than 1 minute to deploy and protect any custom site (or web app), since the course comes with ready to go configs and scripts too.
You could use CloudFlare's flexible TLS, but it's unsecured from their system to your site, which has resulted in carrier level content being injected[0].
[0]: https://news.ycombinator.com/item?id=12091900