The controls have changed a bit from 1.4.7.
By default the menu key for VoxelMap is equals ( = ), the default waypoint key is minus ( - ), and the default key for the large map is right bracket ( ] ). These controls can be configured by pressing the "controls" button from the minimap menu ( = ).
To delete a waypoint just open the minimap menu, click waypoints on the bottom right, select the waypoint you wish to delete, and then click delete at the bottom.