I take it you did not see the large sign at the front door before you arrive at the check in desk ? If memory serves its about 3 foot square...
In one way taking the levy at the desk is a more fair system than adding it to the ticket. If you dont travel you dont pay. How much taxes do airlines keep for themselves from passengers who do not travel ? Smaller airports have to give discounts to airlines too, to get them to operate. Im sure Aer Arann pay very little to Waterford for handling and landing and the levy goes somway to balancing the books.
The main reason airports are taking it at the desks is that it goes straight into the bank account, as you cant trust airlines these days.
In 2003 Waterford had this charge as part of the ticket, From what I remember (could be wrong) Euroceltic troddled away leaving Waterford owed about 40,000 in unpaid levies ! - Money in the hairbrushes pocket
5Q