I didn't see a lot of use for them beyond naval engagements until I joined one of these discussions once upon a time. I always figured that a guided missile should be able to choose it's target within a stack.
Anyway, like everything else, it's situational. If you're like me and produce most of your military units in a few specialized production cities , you can convert all of your other cities ,even those without a barracks, etc., to cruise missile production ( because they can't get exp. points or promotions ) in an emergency, or when your city has nothing better to do. Think of it as spamming disposable cats, except that these things can fly to the city at the front in one turn. Unlike cats, they can have complete kills. So they are especially useful if a war breaks out on an unexpected front and you need to shift assets in a far-flung empire. Just stockpile them. They make great gifts if you want to shift the balance of power somewhere on the planet.