In most Western countries the most senior person in command is a civilian, not a general or admiral (and there are civilians in various other positions, too).
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.