Why aren't larger airliners such as the A380 more efficient than smaller ones?
The comparison is seriously flawed.
While over the entire duration of the flight the larger aircraft is more efficient per passenger/mile, this is not the case for the flight phases that cause the bulk of the fuel consumption for smaller airliners but only a fraction for larger airliners: takeoff/climb and descent/landing.

A 747 or A380 flying a one hour leg, which is typical for many smaller airliners, would use more fuel per passenger over that leg than does say a 737 or A320, despite being more fuel efficient at cruise altitude (if it can even reach its optimal cruise altitude over that distance).

It is also far less flexible, and requires a higher passenger density than does the smaller airliner, a passenger density that's simply not there on most routes unless you greatly reduce the frequency of flights (in which case you'd best hope all your competitors do the same as passengers are less likely to be happy to wait for your one flight a day at noon when they can get to their destination at 8AM taking another airline's flight).