If you want to delete a waypoint that has already been set, simply select the waypoint and click the waypoint icon a second time. A trash can appears and the button turns red. If you click the trash can, the selected waypoint will disappear.
When you delete a waypoint, the card you used to set it is not returned to you. You will need to spend a new waypoint card in order to set a new waypoint.
If your route consists of several waypoints and you delete one of these, all the waypoints that follow the deleted one will disappear as well.