It's faction by faction, and only applies to Mists of Pandaria factions.
The August Celestials
The Golden Lotus
Operation Shieldwall/Domination Offensive
Kirin Tor Offensive/Sunreaver Onslaught
Shado-Pan Assault or whatever the new raid rep was called
Order of the Cloud Serpents
The Black Prince and any pre MoP factions are not affected.
At revered you can buy a grand commendation for that faction, which will double all reputation gains on your battle.net account, meaning not only can alts grind out the rep a lot faster, but even your initial character's run to exalted will be much easier. But you have to actively buy and use the item, it won't apply by default.