You have to remember that the passengers on ORK-AMS fall into four categories - inbound point-to-point, outbound point-to-point, inbound connecting and outbound connecting. Now, if you lose the connecting you're left with the point-to-points.
Open one of the free-sheets like Spits or Metro in Holland and you'll often see ads for Aer Lingus. Also, they have long standing relationships with many Dutch and German tour operators who bulk-book onto the flights. How many Amsterdam-originating passengers will be aware of never mind booking the Aer Arann/Nex Aviation flights?
Even with a much smaller aircraft, I doubt you could make ORK-AMS point-to-point viable. With no service from Shannon, you can credibly say that Cork's hinterland for the flight is Cork, Kerry and Limerick. Those three counties have a combined population almost three times what you'll see in Waterford, Wexford and Kilkenny combined. While there will also be Galway-originating traffic the combined, you can add in the populations of Galway, Mayo and Clare and still not reach the total population of the three counties. And all that's before you factor in people from the Waterford and Galway hinterlands choosing to fly from Dublin or to a lesser extent Cork because of the better timetables offered.
Admittedly, for Aer Arann, this is a no-brainer. They take a cut of the money while Nex Aviation take the risk.