Airliners are optimised for making money.
Also, if you remember your primary school maths you will know that a circle encloses the largest area of any shape.
However, I do agree that this is a far from ideal shape for a fuselage cross section in terms of operation and comfort. I'd say it's an aerodynamic thing.
In modern airliners the below floor area is used for carrying luggage: what struck me when I went aboard a part-stripped 747 was the massive space above the false ceiling.
I wonder if a compromise could be reached such as the oblong fuselage shape of the Avro Lancaster/Lancastrian? Anyway, people seem to be talking about blended wings. (But not doing anything about it.)