Phil,
It is really the same, or similar argument to flight refuelling. It is easier to get planes from A to B in one hop rather than rely on several aircraft/hops.
A direct flight will do the point to point in 2-3 hrs less, and probably much more, than staging.
May I ask another question of you?
You plan a fortnights holiday in Orlando. Do you look for a direct flight from Gatwick or one from a regional airport to Schipol to Detroit to Orlando?
The direct flight is cheaper in costs too. Only one start-up and one climb on the one segment rather than 2.