Sure,
Beginning at the end, submarines? Assuming a submarine could be engineered to not only carry a naval air wing, but launch and recover aircraft in combat conditions, it would be just as vulnerable because it would have to operate on the surface - unless, of course, we plan on trying to make aircraft that can be launched and recovered underwater.
The solution is outlandish, but the threat isn't well argued either. The author spends many paragraphs in the "ships: expensive and manned" and "missiles: cheap and unmanned" sections telling us the obvious but not explaining how any of it constitutes a threat. Just because something is expensive - a "capital" asset and just because there is potentially a lot of relatively cheap ordnance that might be thrown at it does not mean that expensive capital asset is a dinosaur on the battlefield. After all, AAA and ground fire are historically the greatest threat to aircraft, but all that cheap ammo doesn't render aircraft useless.
The basic problem with the essay is that it assumes the weapon system will operate perfectly and the target is unable to do anything about it. Think of the tank example again. There are a million ways to kill a tank today yet tanks still have a lot of battlefield utility. Why is that? The same answers apply to ships.
Getting back to the essay, things get a little bit better with "satellites change everything" but the author makes a fundamental mistake when he says: "We can sit at our desks, type in an address, and have Google Earth show us the current view. It will be a simple matter to find the exact grid coordinates of any ship anywhere in the world, punch the data into a missile silo, and launch a barrage of missiles to the precise location of the ship or fleet." Well, no. If any of that were true, we'd have had that Somalia piracy problem wrapped up long ago. You can do that for immobile targets, but that's not possible with moving targets even assuming Google Earth can show us real-time simultaneous satellite imagery of the globe, which isn't currently possible.
Then there is what is sometimes called the "sensor-to-shooter" problem. There is always a time-lag between acquiring adequate targeting data and weapon launch, not to mention weapon time-of-flight. These time lags can be significant and reducing them is a goal the DoD has thrown a lot of money at. Each second that passes reduces the quality of that data for moving targets. If too much time passes then the weapon will miss. While we work to reduce that time for us in order to more effectively employ our weapons, we also work to increase it for our enemies through a variety of means.
The section on countermeasures is completely wrong. First of all, our response is not limited to what the author lists - a ship's last line of defense. Again the assumption is that we can do nothing but sit there and shoot at incoming missiles until those defenses run out of ammunition. In reality, we have many more opportunities to prevent those last-ditch defenses from even being necessary. What actions we could take depend on the particular threat, but we'd be doing several things simultaneously to mitigate the threat. Here are a handful possibilities listed in no particular order:
- attack the launch platforms
- attack the command-and-control system
- attack whatever sensor network collects and processes targeting information.
- Be tactically proficient (ie., use range, weather, deception, EMCON, etc. to our advantage)
Obviously every threat is different, but the point is that we wouldn't simply sit there and put ourselves into a simplistic situation where whoever has the most missiles wins.
Now, a lot of this is coming about because the Chinese are turning some of their older road-mobile medium-range ballistic missiles into conventional anti-ship ballistic missiles. These are called the DF-21D if you want to do some research.
Here's a primer on some of the challenges of employing ballistic missiles against a ship. Suffice it to say the technical challenges of simply guiding the warhead after the missile is launched are significant even without the problem of collecting timely, precise and accurate targeting information. Let's assume the Chinese make the system work. That does not make a surface Navy obsolete because, again, like any weapon system, we can adapt our tactics and attack the system's vulnerabilities through a variety of measures.
Anyway, I hope that's clear. I have a tendency to ramble. The long and short of it is that any contest between a ship, tank or whatever and a threat is NOT determined by a simplistic rock-paper-scissors calculus.