The author understands their is a misconception at play, but it's not that the public thinks NSA agents aren't upstanding or law-abiding, it's that NSA agents think their idea idea of patriotism is broad enough. It's telling that he dismissed an examination of patriotism, because that's the root of so much discord over civil liberties and national security.
There are two major currents of patriotism in this country. The first is that we take pride in our accomplishments, and we must defend our borders, protect our treasure and lives, and maintain the status quo. The second is more idealistic, that we take pride in having an open (vulnerable, ever-changing) society, and we must defend our democratic identity, promote participation, protect individual freedom, and be skeptical of concentrations of power. The first is practical, easy to quantify (and therefore appealing to a data-thirsty culture). The second is strategic, asks more from the average citizen, and rests on an understanding of alternative forms of society (what is lost when we prioritize security and order over those "inalienable" rights).
Ideally, the NSA would be staffed by patriots of the second type. They'd embrace 'public service' as having deep reverence for the public (not just their physical safety, but their liberties as well), that appreciates the philosophical underpinning of democracy (including it's necessitation of vulnerability and cultural evolution), and that prides itself in taking on their intelligence goals while ardently building checks and balances. They'd never just ask how they can get the information, but how it can be done in a way that proudly upholds American values. With bureaucracy you'll always have some amount of inefficiency and misalignment with top-level goals, but a pervasive culture can go along way.