If someone became insecure due to their face, breast size, penis size, or whatever else, it's all under the umbrella of "insecurity" or "inferiority complex." If a person becomes angry or more motivated due to race, gender, being poor, handicapped, etc. this society actually encourages it. If you were very obese and use that as motivation, that's a good thing, so why did society come up with "short man syndrome" and Napoleon Complex" for short men? What about when a big tall guy's size motivates him to bully others, what's the complex for that?
If we were to pose these questions to society, people will probably claim short men are so much more nasty on average that the stereotype exists. I'm not sure what other genetic trait qualifies for such treatment though. Name one other trait that would cause the average, modern day "egalitarian" to claim a human being born with it is more likely to be evil, like a cartoon villain. Maybe red hair (gingers have no souls)? Although I'm pretty sure most people don't actually believe that one. I'd hope so anyway. People definitely think short man syndrome is real though.
If you were to ask me about all this, I just think people dislike short men so badly that they bothered to create exclusive stereotypes about it. There's a reason why people hate muscular short men, short politicians, bosses, cops, etc. Short men are expected to stay in line and not rock the boat. Certain behaviors are simply off limits.
It's funny too, because I think the average person realizes society doesn't view a 5'0 tall man the same way as an average height or tall guy. Yet when a short man becomes sad or angry or ambitious over the inferior treatment, people act like it's ludicrous and deserving of shame. In reality, literally every group would react this way, as can be seen with any other trait regarded as lesser. What would be crazy is expecting zero reaction when mistreating someone over an immutable trait.
It's actually amazing how most short guys are so obedient in spite for all this, yet this society is still not happy due to its prejudice and confirmation bias.