> Basically, a modern fighter plane is a flying CIWS, if it has the software to do so.

No, it's not, because it can't change targeting axis fast enough; you'd have to have a turret mounted gun plus software, which is simply not feasible for a fighter.

Also, a major surface warship can afford to expend a lot more weight of ordnance defending against a single missile than a fighter can without sacrificing whatever mission it was protecting itself to accomplish.