OK I went back and re-read it and now I remember. Mari's mum cheated on her dad, then left him, and Mari went with her mum instead of her dad. (Why??) Then her dad dies before Mari can ever apologise to him after realising that she made a huge mistake. So that's why she wants to be a puppet controlled by Kon; she has incredible guilt over her choice, and doesn't want to or is even incapable of taking responsibility for making choices. If someone else makes choices for her, she doesn't have to feel guilty if the choices are wrong.
As for her fear of men... I mean it was partly explained at the start that her upbringing involved almost no contact with guys, so she's not used to being around them, and going to a co-ed school around the time she hits puberty certainly makes it worse. Add to that it seems like her mum has given Mari a complex by warning Mari to never fall in love with flashy guys... for some unknown reason? I mean mum was the one that cheated on dad, so why is mum warning about getting involved with guys?? The story would make a lot more sense if the dad cheated.
Also it sorta seems like Mari has just magically become better at talking to guys? At some point she seems to have become fine with interacting with both Seki and Pon, even after Pon became all buff and manly. Idk, I think there's potential here, but so far the writing/story is not impressing me that much, ESPECIALLY considering the reputation that Aka has.
Of course, all of this said, I'm complaining about a manga that I'm reading for free and is being translated for free, so who cares what I think, lol.