By "androgynous", I'm going to assume you are referring to both physical appearance and the behaviors of the characters. If that's the case, then the appeal, or lack thereof, of those characters can simply be explained by personal preference, like appeal for any other character type. Of course, there are probably explanations for why people prefer certain characters. While that would require a more complicated discussion, I seriously doubt insecurity is a significant factor.
By the way, while many people may not like androgynous characters, I don't think that's the main reason people dislike JRPGs. But that's another story.







