Why is the genre so unpopular? ...and for some a Guilty Pleasure?
As one might effortlessly predict, many people seriously detest this genre/trope. It might have to do with the oft-idealised nature of relationships in the anime/manga culture, along with the fanbase's obsession with purity — a phenomenon apparent by the popularity of tropes like Sacred First Kiss, Yamato Nadeshiko, My Girl Is Not a Slut or Moe. That is to say, Otakudom seems to have a strong connection with a specific, sugary perception of romantic relationships, built around pure, sincere, genuine commitment. Hence Netorare, being at the opposite side of the Sliding Scale of Idealism vs. Cynicism, tends to rub people the wrong way. In spite of all the hate, some people are genuinely attracted to this kind of story, for various reasons. Inversely, most fans of the genre are also obsessed with purity, which is what makes it all the more enticing when that purity is broken.
There's also the fact that much of the genre is the emotional equivalent of Torture Porn, so even people who aren't that interested in purity get squicked. Adding more to this is that a blackmailing someone for the sex is VERY common in these kinds of plots, which usually would be a lot more enforced against in real life (being the serious crime known as sexual extortion).
Cuckold the Genre
Expanding the analysis above and using Cuckold trope as a source on why Netorare is more hated.
Many female love interests take the form of an ideal woman. They would often be the Yamato Nadeshiko/Moe girlfriend, childhood friend, or a married woman. As explained above, all of them invoke an aura of their typical womanhood purity (especially in Japan where the traditional view is strong). Seeing them becoming corrupted and promiscuous invoke the fears into the male audience on women breaking the barrier of their cultural standards.
However, another factor in the hatred of Netorare is the degradation of males' self esteem. Commonly, the male protagonist is involved in a situation where they are unable to do anything when their girl is taken away by another man, and often they are forced to witness the girl slowly becoming corrupted (aka a "slut"). The girl's reasoning to choosing the new man is because he is a "good lay" while the male protagonist is unable to satisfy her on the emotional and especially sexual level. The typical ending to visual novels and hentai is where the male character is left off in his miserable and pathetic state as a lonely virgin (or simply loser) while the girl is whisked away having wild sex with one or many men. With the lack of confidence and self-esteem to do anything for their lover, it arouses sexual jealousy from the males, hence the most common phrases or thoughts are "why won't you do it with me/I'm the one you're supposed to have sex with." It also goes back to the old views of the cuckold - someone who sleeps with another man's love interest will receive massive victory over the man who has been cheated which leaves him humiliated and victimized. While that view is not outright shown nowadays, that stigma is still intact psychologically.
Thus, Netorare is essentially cuckold as a genre, but taken to an extremely brutal level. It not only induces a depressing message regarding love and trust, but it also murders the male audience's perception toward women and their own masculinity - ie. someone who cannot satisfy their lover is a loser. And given that the protagonists are supposed to be characters the average male fans can relate to, the reactions are to be expected.