While passing through an unnamed airport in Canada, my wife happened to mention something about her knitting and the fact she wished she could bring it along on the flight, for something to do. The reply she got from the CATSA folks was that knitting needles were fine to bring, as long as they actually had knitting on them. She asked them to confirm; they confirmed. Apparently, a few yards of kashmir wool turns a foot long length of sharply pointed steel from a potentially lethal instrument into an, "oooh, isn't that pretty? You go right on board and finish that sock, and have a good day" sort of thing.
As for explosives, we in the military aren't alone in our troubles. Mining contractors (I came from the mining business, so I know more than a few) are constantly getting pinged with positive hits on their baggage, clothes and even skin and hair. If you work with explosives day in and out, traces will come to permeate your person. Mining guys have generally accepted this and identify themselves as soon as they hit security.
I agree that the guy was doing his job in the OPs post. When I travel in uniform, DEU or combats, I stand ready to do whatever the security folks ask me to do (well, within reason). That includes taking off my boots. I look at this way...I'm putting on a public face for the army, so the way I behave and react matters. If I'm cooperative, then I like to think it becomes a bit of an example for those around me. I've actually had other passengers express dismay at my being searched ("he's a soldier, for pete's sake!") but I just tell them not to worry, that I shouldn't be treated any differently, and thank them. It helps with the footprint in the community thing.