While it's true that fighter jets have been aerodynamically unstable for decades, they're not built for transportation and have ejection seats.

The main reason they are unstable is to increase agility. Is this necessary or even wanted in passenger aviation? I don't know but I'd guess not. Probably safety, comfort and fuel economy are far more important and can (should?) be achieved with a stable airframe.

fighter jets are the more extreme and established example, it also applies to most modern airliners which have software systems in place to prevent human controls from exceeding the aircraft flight envelope

fuel efficiency in these modern aircraft has been gained with swept back wings, larger intake engines etc. which with direct control and no software would be almost impossible to keep flying

discarding all of these systems because of a problem with one would set airline safety and efficiency back decades

Swept back wings and larger intake/bypass engines does not make the airframe inherently unstable.

The fly-by-wire system has multiple redundancies and layered protection, including direct law (at least for Airbus). Fly by wire is, like you say, of course a great innovation for improved control and safety, but it's nice when the plane continues flying even during a failure, however unlikely.

I guess in the case of MCAS the software was activity working against the pilots so maybe it's more of a problem with the design of this particular system and training.

I wouldn't hold fighter jets up as an example of safety. They spend more time broken then they do operational. Require a an entire team of engineers for each airframe, and the number of pilot deaths/flight time is pretty atrocious. But since it's 1-2 pilot deaths rather than >100 passengers we put up with it.

A well designed aircraft should not have a single point of failure, including the software.