Misogyny carries at least two different meanings now, M.J. As you know, its etymology is "hatred of women," and it retains that sense: that's why it stings to be labeled as a misogynist.
But there's a broader, maybe "softer" meaning that Kaia Maeves clearly alludes to in her comment below, in which misogyny is a "subconscious" bias and the result of "systems that we're all born into." In that sense, misogyny does not seem like a personal animus or hatred, a cultivated bigotry, but a set of blinders that we've inherited and that, with curiosity and better information, we can put down.
Are you a misogynist in the active, hateful, bigoted sense? Absolutely not. I'm comfortable saying that this piece itself is sufficient evidence.
Are you a misogynist in the subconscious, socialized sense? I have no idea, but probably less than most of us. Your self-examination and resistance to defensiveness argue against it.
Was that commenter off-base, a poor reader, and a righteous Medium troll? Without a doubt.
Examine yourself all you want, my friend, but not in response to misplaced indignation.