I'd already read this article, and refrained from posting about it.
As gf0012 said, most of the relevant information is classified, and Thompson provides mostly anecdotal evidence.
My gut feeling, though, is that while it's certainly far from being as unprofessionnal as Thompson implies, the US Navy - and the Army and Air Force as well - are probably overconfident.
I frequently read US officers posting on fora such as this one who are unbelievably dismissing of everybody else's armed forces. A marked superiority complex is definetely not a good thing to have when going to war.
It is true that for the past 50 years, the US has enjoyed the ability to pick its fights, and has picked them rather wisely - from a conventional warfare point of view, the political/LIC side is open to much wider argument.
Therefore, for half a century, US armed forces have only met on the field of battle forces that were markedly inferior. This strategic success emphatically does not imply tactical and operational "ultimacy". Yet more often than not you will hear or read that implication being assumed.
Much is made of the US technological superiority, too. What is meant there, though, is mostly electronic and IT-related technology. While transistors, integrated circuits and software certainly have stupendous military value, they are not the be-all and end-all of military technology. And the fact that you've - successfully - spent a lot more R&D money than the other side doesn't necessarily imply a congruent superiority. I am reminded here of the US and Soviet solutions to writing notes in zero-G in the sixties. NASA spent a respectable sum of money for a ballpen design that would work without gravity. The Soviets gave their cosmonauts pencils.
And it took the fall of the Berlin wall for the West to discover that the technologically inferior Soviets had much better kit than us in some areas - I'm thinking about IR and passive aircraft detection systems.
The gist of this is, while I certainly can't conceive of anybody today who could seriously challenge the US militarily, be it on land, sea or in the air, the US should nevertheless be wary of nasty surprises the day somebody chooses to challenge them and not come to this fight the way they went into the Pacific War.