For the protection domain power:
...In addition, you receive a +1 resistance bonus on saving throws. This bonus increases by 1 for every 5 levels you possess.
And similarly worded powers like the Aristocracy domain power:
Noble Visage (Su)
You gain a +1 bonus on Charisma checks .... This bonus increases by 1 for every 5 levels you possess.
Is the bonus based on character level, or cleric level? I'd normally assume cleric level, as it's a class ability, but elsewhere in the protection domain (and some other domain abilities), it explicitly lists cleric level:
Aura of Protection (Su) ... The deflection bonus increases by +1 for every four cleric levels you possess beyond 8th.
So I figured I'd get confirmation.
Class abilities go by class levels unless otherwise stated