Magic protection protect against FUS RO DAH?
No. Magic Resistance and Magic Absorption only apply to the actual damage that is dealt by a magical spell or shout. Thus while it will mitigate the damage that Shouts will deal to you, as the stagger is an effect that is separate from the damage, it will not.
Source: Turned on console commands, got 100% Magic Resistance and 100% Magic Absorption chance with crazy enchantments and still got staggered.
However you can use wards to block it