There are 2 main reasons:
The wing spars run through that area. If you wanted to keep the wing spar within the oval cross-section, you'd have to install the wing much higher on the fuselage which means the wing spar goes through the passenger cabin.
Behind the wing spars, the landing gear is stored. The flat bottom provides more internal space.
Hobbes' reply has some of the main reasons, but there's some more:
That flat bit is called the "belly fairing", and its functions are:
Avoid some aerodynamically awkward corners that would happen if the wing profile just went straight through the fuselage, with no rounded corners etc. at the intersection. This is particularly useful at the wing ...