I can only speak for myself, but I use the term obviously realising there is no such thing. I use it to describe the man I spent two years of my life with (I was going to* marry * him), who literally, truly blamed everything “wrong” in his life on the fact that he was short. It’s not what broke us up - he left me for another woman. I didn’t pin any of his shortcomings on him being short, he did. This is what led to my husband using the term “short man syndrome”. I thought it was pretty obvious it was a joke term used to describe an angry, little man who was angry because he was a little man.
He didn’t work out at all, or drive a big vehicle. He was pretty damn well hung, though - but he was *still * angry! 
On the flip side, there was a guy I went to school with. He was tiny - under 4’! People use to tease the hell out of him, and call him “Smurf”. This guy never once got angry at anyone for it, he always smiled, shook his head, let it all roll of his back. He drove a pretty damn big car, and he worked out quite a bit. I didn’t get along with him because of an argument we’d had years ago. I would never once say he had short man syndrome. And very few people would.