So I installed the plugin vanilla and didn't change anything.  It looks like it is already set up to flip permissions on and off when a player sets a waypoint.  If they try /wphelp, they get "Unknown Command".  If they type /setwp name, they get "you cannot use this command".  I'm thinking I missed something obvious but don't know what.

"you cannot use this command" means you don't have the personalbeacon.use permission

How do I set that for all users?  I was under the impression that line 163 (permission.RegisterPermission("personalbeacon.use", this);) covered that.

No, permissions must be assigned by the server administrator.

oxide.grant group default personalbeacon.use