Femmephobia is an aspect of misogyny, yes. But it's also an aspect of things that aren't traditionally considered misogyny. As mentioned in the article above, femmephobia impacts all femininity, no matter how the femininity is embodied.
In Whipping Girl Julia Serano distinguishes between oppositional sexism--the notion that men are better than women--and traditional sexism--the notion that masculinity is better than femininity. Second-wave feminism, and to a degree some aspects of third-wafe feminism, tend to conflate misogyny with oppositional sexism more strongly than traditional sexism, which is why butches and trans men are often positioned as being radical, while femmes and trans women are often positioned as being reactionary. I'd rather see misogyny encompass both forms of sexism. Gradually that's becoming the case, but we still have holdovers.
As a queer trans woman, I'm painfully aware of how more masculine persons behave towards the feminine. It's all the more reason for me to possess a vocabulary to properly describe the experience, and the tools needed to respond in a more empowered way--and to share them with others who might have need of both.
