You have to look at total cost per ASM (ASK), not just fuel. Certainly the 380 is a fuel hog, but if fuel stays below $75 other factors begin to become more significant, driving the seat mile costs closer to that of a big twin. I fly for an A380 operator...passengers actively demand it over the well-appointed 747s we also fly.
Your comparison on frequency is broadly correct, but your example is based on short haul realities rather than long haul. Over great distances frequency is often once a day.
If you compared a carrier operating four 737s, you'd need to compare than to one operating three A330-200s. No prize for guessing who wins that one on passenger appeal.
Passengers in most parts of the world prefer wide bodies. Enough to overcome a slight frequency disadvantage on routes of over, say, two hours. And passenger behaviour cannot be predicted on purely rational expectations.