I beliieve that some charges such as landing fees were reclassified as surcharges by airlines a few years ago as no commission was paid to travel agents. It also meant that they started receiving serious sums for passengers cashing in frequent flyer miles.
In my experience as surcharges have increased the basic fare has dropped so that it could be as low as £5 for a legacy airline between LHR and AMS. OK more passengers include the weight of an aircraft, but fuel is a largely a fixed cost so airlines will make much more than this amount by selling an extra seat.
If we move to per departure air passenger duty presumably airlines will have to include it in the basic fare. Well possibly...