Protect won't proc even if enabled.
I've tested this in both PvE and PvP settings.
I've tested with the mercenary Alma, a character who's a BK, and Engineer's Metalaegis.
Basic hits--ranged, and melee are not protected against.
Autohits--ranged, melee, and magic are not protected against.
Here is some relevant information I dug up:
It seems that the problem has persisted for quite a while.