Master of Shadows |
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Emphasis Mine:
PRD: Protection from Evil wrote:
First, the subject gains a +2 deflection bonus to AC and a +2 resistance bonus on saves. Both these bonuses apply against attacks made or effects created by evil creatures.
So with the wording above its pretty clear that it is intended to apply only against evil creatures. The second sentence provides the necessary context despite the fact that it does not include the qualifier ONLY between the words Bonuses and Apply.