Because reality doesn't always generate the most interesting stories.
For a story to work, the audience needs to be able to connect on a certain level with the setting or characters. It doesn't matter how well crafted the situation is if you don't care about what's happening. In School Days' case, I found it hilarious actually-- sure what occurred can and will happen in real life, but the characters were really too thin for me to take seriously and I found it over the top. It doesn't help that the writing was rather lazy and they ...
Personally, I think a lot of the negative reception for this anime had to do with the execution since on paper, School Days actually had a pretty novel concept in regards to harem anime.
However, it is true that more realistic characters are more polarizing. Essentially, protagonists that don't fit into protagonist roles tend to get bashed very heavily. It seems the concept of good people doing evil things doesn't seem to register in many people's minds. Also, in a number of cases, people get offended when a character fails to do what they would have done, because it's "stupid". In other words, people have trouble tolerating others that perform certain actions. They don't want to take the time to consider the context of the character or why they are what they are. In other words, viewers often force or project their own expectations on the anime because thinking critically is hard.
Then again, given that many people who seem to want to dictate what people do in real life, this hardly seems unusual.
Of course, if one wants reality, they can just look at the window and entertainment shouldn't always have to involve deep thinking, so that's may be why many don't care.
In any case, OP, I found this thread interesting because I'm watching an incredibly painful and realistic anime where the characters and story can be extremely polarizing. It's called Nana and you might want to give it a try. I think it really runs on a much higher level than many romance anime.