I think for the most part it's because Sasuke represents everything the reader is supposed to dislike. His self-centered, conceited, and over-confident with his abilities. He also obtains abilities rather easily... not that he doesn't work hard to obtain or master his skills, it's just easier for him to do so than, say, Naruto who works ten times harder.
One of the original points of the story was a flunky comparing with a genius. Naturally Naruto represents the more human side, failing 9 times out of 10 only to figure things out through hard work and determination, while Sasuke was capable of succeeding on his first try (most of the time).
As a character, he's meant to be hated by the fans, but with a backstory to try and convince readers to partially understand him. Sasuke was a kid who adored his brother and wished he could be like him and receive the same kind of praises - but turned out that his brother was a cold-blooded killer. His decent into darkness happened because he wanted to be strong enough to defeat Itachi, but everytime he sees Naruto improve (refer to the first time he saw the true damage of the rasengan) he gets angry because he feels like he's hit a plateau and now even a "flunky" is "catching up" with him.
That eventually shifts into a plot twist when he learns of the truth behind Itachi and hatred is reborn. Konoha had no clue about Itachi's true motifs and as such always referred to him as a monster. Sasuke - out of love for his brother that he originally adored - decided that they had no right and wants revenge, if only for his own means.
Like I said, Sasuke came to represent the kind of character a reader is supposed to dislike. Though it doesn't help when you have fanboys obsessing over him all the time, but the came could be said for Itachi, Minato, Naruto, Neji, Madara, Tobi, etc.. any fanboy can be annoying, no matter who it's for.