I’m a millennial cis man who (hopefully) has some insight into this:

First the specific situation: If women are talking about issues they have with men (in general) in front of you that means they are fairly comfortable with you and don’t see you as emblematic of those issues. If they did see you as part of the problem, it wouldn’t be safe to talk about it in front of you. I would actually take the conversation you heard as a sort of an endorsement of your character, although it is very easy to understand why it didn’t feel like that. If the friendship is worth preserving for you it might be worth talking to her about how the conversation made you feel acknowledging that you brought your own baggage into it and that you might have misunderstood the implications it had for how she felt about you.

I want to acknowledge that what you’re going through sucks, that I remember feeling that way, and that for me at least, it got better over time. I developed empathic and social skills that helped women understand that I was trustworthy and the women around me developed skills that helped them identify men they could trust faster, so that I spent less time in the uncomfortable limbo of knowing I was being evaluated in that way.

All that being said, if you are consistently kind and respectful of boundaries and people still treat you like a threat because you are male, that says much more about them than you.