I agree completely with Darkshine.
SPOILERS!
The whole plot of School Days revolves around a love triangle, and sometimes other characters get in the way too. You "have" to cheat on others, otherwise there would be no story.
Makoto is a very indecisive guy, and initially just planned to stay with Kotonoha. However, when he realises that nearly every girl on the school likes him, he doesn't know what to do. He tries to follow his heart, but it's extremely difficult since he doesn't want to hurt anyone, and isn't very sure of his real feelings, either. It's already confusing for a fictional character, imagine for a real person. I wouldn't know what to do in this situation.
But the real problem is that he is an absolute jerk in the anime.
People think that it's the same thing in the VN. That's not right.
I dislike the anime for a few reasons. The opening and ending have changed, and I don't like them at all. The animation quality and character design is inferior, and there's also the fact that some characters have a completely different personality.
Anyway, all characters in the Days series have faults, and that's what makes them better and more realistic. I agree that the harem setting isn't very realistic but the other situations are, in my opinion.
Kotonoha herself is troubled. She can be incredibly obsessive sometimes, and this is evident in a few routes. She hurts Makoto a lot, too.
I've completed the game three times, I believe. I got the Bloody Conclusion, then the New Year's Eve ending, and more recently, Bavarois.
It's not fair to hate on the work itself just because you dislike one thing. I see a lot of people criticizing films because the characters are absolutely insufferable. I guess if it makes you feel something, be it either love or hate, they've accomplished something, right?
I know it can be hard to continue if you don't like the characters or the story, but at least in the case of School Days, you can change what happens.
Anyway, there's always plenty of other films to watch or other novels to read. You don't have to stick with something if you don't like it.
