More of a wetware problem....
One point I think the article doesn't drive home among the others mentioned is most of these attacks that span the air gaps require a bad actor to physically touch the systems. The malware doesn't magically materialize out of "thin air" some one had to put it that environment, weather it is hidden in the hardware at the factory, typed in from memory or uploaded by a flash drive there is a human behind it and there are well documented process and methods for protecting against these types of attacks, primarily by limiting access, requiring a minimum number of people to be in the room at any given time, division of labor, mandatory access controls, rotating the employees assignments and shifts to prevent collusion, monitoring of employees activities inside and outside of work, and limiting what is and is not allowed into the environment (e.g. no cell phones, electronics, paper, pens, etc.).
When the proper controls are in place and and properly managed the risk of data ex-filtration across an air gap is greatly reduced. Most incidents of this type that I have investigated are failures in physical security, and lets face it once you have physical access to the box it's essentially game over, there is no limit to what you can do at that point.
Mine's the one with the usb cufflinks.