The correct use for Cruise Missiles is to aim them in the general direction as the person you're mad at and watch them splatter his forces all over the terrain.
Of course, at this point we've got a whopping one unit that actually packs a Cruise Missile Launcher- the super Sturmfeur from XTRO Corporate, which mounted a single Cruise Missile 50. Kind of a waste, really. If you're going to have to use ammo haulers to pack the ammo around, you might as well just go with a static launcher anyway, because the vehicle's not giving you any benefit.