ATC won't normally issue a "direct" clearance to something other than a beacon (ie an intersection or any other waypoint) unless they see from your flight plan that your a/c has the appropriate equipment. If in doubt, they'll ask you something like "can U accept direct xxx ?".
Most airliners use a system called INS or IRS, which does not need any beacon or any external signal. All U need to do is enter the intersection/waypoint name or, for slightly less sophisticated systems, its lat/long.
Light GA a/c can B fitted with either GPS or a system called RNAV. With the latter, U enter the coordinates of your intersection/waypoint in relation to a specific VOR. U need to enter both the distance & the bearing. Once U've down that (& activated the RNAV), the VOR is virtually moved to your waypoint & the nav reverses to a dead easy VOR tracking with TO/FROM indications & normal needle deflection.
MF