why not? rulers can promote national religions, but dukes or even ordinary lords can make additional effort to oppose it. is it not good opportunity for development of interesting grievances? hostile religions can always be banned, so taxes could be mid-solution that allow more nuances of possible conflicts.
if all agree about single religion, all will promote it with or without taxes. however, if there would be disagreement, mechanics would fuel conflicts.
i always believe more power is good if there is a chance to oppose such power. on contrary, removing power from most of positions can sterilize conflicts.
This would entail allowing individual religion taxes at both Duchy and Realm levels and possibly region levels as well. This adds a lot of complication to the tax system that personally I don't think this feature merits. So far the discussions have been about allowing taxation of the Religion at one level only.
If we have multiple levels of religion taxes how will that work? If Region/Duchy and realm all issue 20% tax, does each get applied to the current religion treasury? Does the Realm tax percentage only apply to the religious taxes collected by the Duchy? In the first we can quickly see crippling taxes being an option upon religions unless we apply strict limits to taxation percentage. In the later I think we need to start modifying the database to store extra info about where taxes come from etc, which probably ends the discussion right there.
