And the military doesn't run the government. That's also a good thing.
The only way your analogy works is if you think it's a good idea to appoint generals and admirals who have no military experience. I hope you don't.
Anyway, why not under certain circumstances? Already now there are differences between countries what is run by the military and what isn't.
Because someone with no military experience is inexpert. They don't know what they're doing.
In the military a lack of expertise is very likely to result in people dying unnecessarily.
The US army corps of engineers being in charge of levees isn't the only way, for example. A lot of generals don't fight wars. And those who do, are under civilian supervision.