The most effective weapon against a cruise missile is an airplane. They fly too low for ground weapons to be effective but if you put enough aircraft in the air with AA missiles, they can take them out. And it doesn’t matter what kind of aircraft or missile since the cruise missiles can’t shoot back. An old F4 with Sidewinders can do the job.
In the first Gulf War I read an account by a reporter who saw a crippled cruise missile fly down his street.