Almost the entirety of the cost of an orbital launch is in manufacturing and operational costs. Cost of fuel is basically just noise. If you can reduce operational turnaround time and operational complexity, even at a cost of payload, then you'll save so much money it'll be worth it in the long term. SpaceX is aiming for a re-assemble, gas up and go workflow. If they can pull it off it might reduce their per flight launch costs by a factor of 10 in the short term and perhaps as much as 100 if they get really good at it (although that's likely several generations of hardware down the line, at best). With that sort of thing on offer a reduction in payload is easily justifiable.

Imagine if somebody replaced your car with a version that had twice the carrying capacity, but would only run for one tank of gas. It wouldn't be a worthwhile trade would it?