I am Currently playing an Asatru Ruler (king) in Bohemia (start date 1066) as vassal of the HRE.
I have religious rights protected in my vassal contract with my liege the emperor.
4 converted counties, owned by my vassals are doing an Asatru populist uprising independence faction against my liege the emperor (my liege, not against me). The converted county owned directly by me is not part of the faction.
So probably the game is checking maybe if the direct ruler of the county has religious protection in his vassal contract, but not if somebody else between the direct county owner and the top liege (me) has religious rights in his vassal contract.