Why are combi airliners no longer being built?
While combi configurations are rare, they do have a place -- for instance, when operating narrowbodies into remote locations which have a demand for cargo that exceeds what can be put in the belly, but also need pax transport.

The most recent combi configuration I can find a source for is the 2008 work done by Aviation Traders to configure Iron Maiden's touring plane.  In this case, they used the existing seat rails to mount pallet fittings in order to avoid structural changes to the floor, and also are taking special steps (such as firebagging of cargo) to mitigate against a main deck cargo compartment fire.

As to why they aren't made otherwise?  It clearly isn't operating economics, at least for Alaska Airlines, Canadian North, First Air, and other current combi operators -- otherwise they'd have retired their combis by now.  The main issue, I strongly suspect, is actually the unsolved problem of fire suppression in large, main deck class B cargo compartments, such as those found on combi aircraft.  Aviation Traders' work on Class F is intended to solve this problem, made famous by the crash of SAA 295 after its main deck class B bay experienced a fire of unknown origin that proved catastrophic.