Things like the Bagram PX were concentrations of high value targets with only one source of supply. The general USB stick marketplace is a lot safer. In China they're often fake and thus unreliable (smaller than advertised), but in the US, I'd be pretty comfortable driving to a Best Buy 50 miles away and picking up a random USB token.
A USB key someone hands you is much more likely to be a targeted attack. A USB key randomly lying on the ground outside a target is also much more likely to be an attack.
That doesn't mean there are no attacks.
So prudence is adviced in either case, on the off chance that the one that you have is a bad one. Ditto for anything else that you stick into a USB port.
That webcam plugged into your computer, are you sure the mike isn't on all the time and that the driver doesn't pass your speech during the day out in compressed and encrypted form to some server farm at night ;)
Oh so he encrypted his files, and walked them between his stand alone and his internet machines. Yeah, okay this established the file's integrity, and that's just fantastic.
But what assurance does he have that the USB stick isn't getting infected on the internet machine, and then deploying stealth hacksaw services onto the standalone, to buffer and relay data and commands each time it jacks in?
I mean, that's exactly what Stuxnet was designed to fucking do.