There isn't a root of evil. Evil is in everyone, and it comes from everywhere. Good creates evil, and sometimes evil creates good. There isn't one central bad guy in all of this. Orochimaru, Danzo, and Madara are all roots of negativity, but even calling them as a whole evil is questionable. Orochimaru is a nihilist who's obsession with jutsu has developed as a result of his parents dying when he was a young child, and then further was developed when he had to take part in a ninja world war. Orochimaru was surounded by death all his life, and that molded him. Danzo was similarly forged in death, and he decided that peace should be acheived by any means. Madara was hurt by war and death even more so than the other two, having been alive at the height of ninja war. He's the most twisted by it because he's seen and done the worst.
These people aren't evil for the sake of evil, and none of them are the only cause of evil in the world. They are merely victims of a ****ed up system that went on to do ****ed up things as a result of it. Madara's character is bland otherwise, but that's because he was introduced so late. The other two have rich, more gray than black characters if you look hard enough.