Flutes are not girly. In the first book of paradise lost, the hosts of hell march at the sound of "flutes and soft recorders". Of it's good enough for Satan's army, I say it's good enough for a highschooler.
The point of the article is that a specific social group thought that they were. It doesn't make any claim about the general truth, just that certain things have social stigmas that may not make sense objectively, but one still lives in that social group so one has to cope with that stigma in one way or another.
There could have been a dozen other examples. Perhaps dancing, or cheerleading, or computer nerding, or whatever else. All of which have had various social stigmas in various groups at various times.
I would like to point to Ian Anderson.
I'd argue that flutes are characteristically masculine what with their phallus-in-hand-demeanor. Though that is perhaps why Manly Men aren't meant to play them.
But perceptions are certainly different.
Several studies [0][1][2] have found significant differences in gendered participation in various instruments, and the perception by others of people playing instruments typically played by other genders.
Further, at least one study [4], has found that this variance vanishes or flips in queer ensembles.
Anyway, I wanted to check because Paradise Lost was a long time ago. Men were the first to wear high heels, after all. I figured there'd likely be a drift from times where flutists were male because ensemblists were male to now where anyone can be seen as gay for just about any reason.
[0] https://www.researchgate.net/publication/264200609_Musicians...
[1] https://digitalcommons.lib.uconn.edu/vrme/vol5/iss1/3/
[2] https://theath.ca/arts-culture/instrument-gender-bias/ (mentions a different study)