Why will my Mac only load Google and Facebook?
In my case the problem was IPv6. Websites like Facebook, Google.com and Youtube use IPv6 and work fine while other's don't support it yet. 

I couldn't figure out the issue exactly (and the right configuration for IPv6) but I disabled IPv6 and the issue was resolved. This is all I care at this point. 

The commands for El Capitan:

Turning off IPv6 support for ethernet:

networksetup -setv6off Ethernet


Disabling IPv6 for wireless:

networksetup -setv6off Wi-Fi


If you ever need to re-enable:

networksetup -setv6automatic Wi-Fi
networksetup -setv6automatic Ethernet


I will edit this if I ever find the correct setting for IPv6 instead of a full disable.