There's an unfortunate focus in the admiral's comments on ship-to-ship warfare, which really isn't something we get a lot of nowadays.
What's deliberately not mentioned is how useful this might be for shooting down a missile at launch. It is, as they say, hard to hit a bullet with a bullet. But hitting a bullet with a much faster bullet...
With a missile coming toward you at Mach 2-3 you don't want to be shooting subsonic cannon shells at it.
The rail gun ammunition is much smaller so you can carry much more of it and make a much more mobile gun turret because it doesn't need to store tonnes of shells or have a feed back to a magazine.
Current destroyer's gun: http://en.wikipedia.org/wiki/5%22/54_caliber_Mark_45_gun
Iowa Class gun: http://en.wikipedia.org/wiki/16%22/50_caliber_Mark_7_gun
The article says "Indeed, a railgun could be used to inflict just such harm on another vessel.", which is true, it could be used for this purpose, but they would not be sinking money into this just for that.