Russians have been working on a hypersonic cruise missile for a long time, so do the US, both have failed. There are a number of supersonic cruise missiles and all stealth cruise missiles in US's inventory have been mostly retired. China, France, of all countries, India, have supersonic cruise missiles which are significantly harder to intercept, especially since 3rd and 4th gen Aircrafts are no longer interceptors and significantly slower than their 2nd gen cousing (F-4 could do M2.5, Foxbat was M3.2). Anti-aircraft missiles are point defenses, they can shoot down a subsonic or supersonic missile but struggle with a hypersonic one.
The original article assumes an enemy (*cough*China*cough*) is going to fire all of their subsonic and supersonic missiles first to force USNAVY to spend their missiles in their AEGIS cruisers and then promptly sink then with their modern, hypersonic missiles. It is possible but not likely.
One thing to remember from WWII: The bomber will always get through.