the best active defense against cruise missiles can be found in a modern aircraft carrier battle groups because they use an overlapping combination of ship-based and airborne surveillance designed specifically to prevent low-altitude attacks like cruise-missiles (and water-based low-speed attacks eg the motorboat used against the uss cole). there are a limited number of systems capable of this method of defense and they are very expensive to build and to maintain actively. until airborne detection systems can be kept aloft cheaply and permanently cruise missiles will remain a significant threat to anyone who cannot afford the systems required to defend against them.