What Are Little Boys Made Out Of?

http://www.boxturtlebulletin.com/what-are-little-boys-made-of-main
I spent a few hours yesterday reading through this site, and it was my first time hearing about something like this. I had, however, previously known that for a while the idea that gender is purely formed from environmental influence, and that there were experiments that the Dr. Green mentioned in this story carried out that were just as horrifying through the lens of today's society. One such disaster consisted of performing sex reassignment surgery on a boy whose penis was ruined during circumcision, and instructing his parents to raise him as a girl (he grew up to go back to living as a man, and committed suicide in his 30s).
Sure, Rykker's thought process is terribly out of date, but he and others like him are still around, and the stigma surrounding boys who act effeminate as children is hardly lifted these days. It is helpful to live in a more liberally minded society, but most of the United States remains homophobic, even misogynistic. "Being a woman" is often used as an insult in itself when male figures in a gender or sexually confused boy's life berate them for not living up to societal standards of masculinity. Femininity is almost understandably undesirable in children, but how is "being a woman" considered a bad thing? It's almost like they believe women to be inherently inferior creatures, and the reason men must "act like men" is because they must do their best to dissociate themselves with something that is totally on a different social hierarchy.
I did find it interesting that no one really spends much time thinking about masculine girls, though. Maris, the sister of the boy which the paper focuses on, mentioned that as a child she often dressed just like the boys, "if not more boyish." Sure, tomboyishness is not a desirable trait, but it seems girls have a much easier time "growing out of it," or at least that's what I've observed. Why are tomboyishness and "femboyism" treated so differently? And why do so few women who start out tomboys actually turn out to be transgender? The obvious answer is that society chooses to ignore masculine women, because "mannish women" are considered unattractive, and in our male-dominated society, only men and women who exist as objects of desire are actually focused on. The lesbians that do not fit the category of "girl on girl is hot" may just drop out of the public's awareness. Meanwhile, gay men are considered threatening to the (insecure) straight man.
I speculate, but I haven't been able to find a straight answer on any of this.