I'm now paused in the middle of a scene that is even more disturbing.
The main character and some other students are spending the night at school in some unofficial capacity (there don't appear to be any chaperones). He hears a noise and peers into a window to see what's going on.
I'm now going to turn to EXACT QUOTES, although I'm leaving some words out in between, and the bolding is all my addition to draw your attention to what's bothering me here.
Hayashi-san[girl] is being pushed down by Yoshida-kun. She's on the floor and I can see her white knees moving a little.
"Ah, mm, no..."
Her seductive voice stops me.
Yoshida-kun, who's on top of her, covers her mouth with his own.
Then his hand runs through her clothes and exposes her breasts.
He closes her knees and takes her panties off with both hands.
Next he reaches to his own belt.
Wait, you're rushing too much. You only touched her a little.
Are you sure? Is there a chance of success? If she doesn't have much experience, then it's too dangerous to attack right now.
I'm cheering on Yoshida-kun[male] when...
... So, again. I don't know if this is an accidental nuance coming through via shaky translation. But the actions and the specific language used give the impression that the main character is actively cheering on rape. Or, at the very least, like he thinks that the correct way for a couple to have sex is for a girl to say no a lot and the guy to take off her clothes and penetrate her while she gives no sign of consent.
And the main character is not written like the author thinks he's a bad guy.
The above quote is the point I paused at to be boggled by the scene, so I'm not yet sure how it will develop from here...