Is it typical to use protectowrap on a deck ledger?
Yes, that was installed for a reason. A common rot location has been behind ledger boards such as this. Even with metal cap flashing water tends to run behind, and it doesn't dry out well. This results in rot of the sheathing and joists behind. 

Normally the siding is close enough to the deck that you don't see the flashing. You might overlay something to conceal the membrane. To avoid fastener holes it could be adhered with silicone or urethane caulk and held in place with the decking.