Also, a SuperDuperBig drink has more 'stuff' in it than a SuperSmall drink but some fast food places have started to have one price for all drinks regardless of size. That's because it makes sense when you look at the big picture of what it costs to sell you that drink. What things costs is not just a factor of what the raw ingredients cost. There are many factors that go into a setting a price. In the case of the airlines, fuel cost is just one of them. Think about these other costs:
Pilots - you need two and that cost is fixed. If there is 1 person on the plane or 100, there are still two pilots (on a jet, not a puddle jumper)
Stewards - that cost is per passenger. Heavy passengers don't need more stewards than smaller passengers - there is no way to measure ahead of time how demanding a passenger will be
The Plane - another fixed cost and the biggest cost - when a plane is first put into service, it's all about recouping the cost of the plane and the rest is noise
Maintenance - relatively fixed, more a function of plane use than how many passengers are on a particular flights and how heavy they are
Amenities - a combination of fixed costs and per passenger costs
Advertising - variable but not based on passenger size at all
Airport usage & other services - relatively fixed, more tied to usage so could be somewhat impacted by # of passengers, but not tied to passenger size at all
Ticketing - there's both the cost of issuing/tracking a reservation/ticket which is per passenger and fixed costs of having a ticketing/reservation/check-in system
I'm sure there are other costs I'm not thinking of and I'm sure they are not based on weight.
I think the airlines have done a good job of selling the public on the idea that it's all about fuel. We all pay at the pump and have felt the pain of rising fuel costs so it's something we can relate to. Plus size prejudice is socially acceptable and most of us had to deal with having a seatmate who doesn't really fit in their seat too and it can be unpleasant. So pushing that angle can work for the airline.
But only up to a point. At some point the public is going to rebel, IMO. As has been pointed out, paying by weight isn't really logistically practical. Are people going to fly an airline that makes them feel like cattle going to market? I think about when I was more self-conscious about my weight and every time I went somewhere I had to be weighed I would play games like wear light clothing and not eat until after I got weighed, etc. I don't really want to be playing those games when I fly.