In real life, are flight plans not always plotted using airways?In looking at routing from KSFO to KATL in Flightaware, there are a series of waypoints but no mention of airways and not all of these are joined by airways. Do the commercial flight routers sometimes bypass the airways and just plot point to point?

Yes, it is common on transcontinental route with equipment that does not rely soley on radios for navigation

Sure. In the real world, flight plans can be from VOR to VOR, which usually follow an airway anyway but not always. You can also fly Direct (if ATC approves it).