These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: Bitter Virgin
Iron Woobie: Hinako, while also being very vulnerable, does have a tinge of iron, starting from the first chapter when an oblivious Daisuke pushes her against the wall, intending to take her up on her "faux innocence" (as he thinks), and is shocked to find her staring right at him, as if resolving herself to some terrible fate. Considering what must be going through her mind, this is simply "Wow".
Also, why is Hinako subjected to rape and/or almost rape several times in the story? Not only it can be seen as very lazy and melodramatic writing... but for some people, it seems to suggest that "a woman isn't truly abused/traumatised/etc. unless said abuse/trauma involves her genitalia". While one can understand Kusunoki's personal reasons, it's still not an excuse for this.
Values Dissonance: Things like Daisuke's sister's pregnancy and Hinako's history of being abused would be nowhere near as big a deal in Europe or America as they're depicted in this manga, so it's important for readers to remember that Japan is still struggling to shake off the whole Defiled Forever concept.
You can't really single out Japan for that, and the way the author depicts this subject doesn't necessarily mean it represents Japan's modern feelings on the issue, or the author's. It's just a story.
Since when, in any modern culture, has the sexual abuse of a minor to the point of pregnancy TWICE, ever not been a "big deal?"
It's a big deal, and being raped is not seen as "the woman's fault" in Japan. However, rape still carries of stigma of dilution or tarnishing, in that a woman has been - against her will or otherwise - ruined, and therefore an undesirable candidate for marriage. One does not blame a faulty product for being damaged by someone else, but ultimately people don't want a faulty product... or so Japanese traditionalists see it.
Fortunately it's not as if the story sees it that way. Kei Kusunoki is firmly on the side of her female characters.