I don't know you got that idea from, I don't think that many people hate him. Loads of characters are hated far more eg. Sakura
As for the main character, he isn't a bad one at all. Sure, there are many flaws to his character, but that's the same for every character. In a story, the protagonist is the one that the message of the story is shown through, the one that is supposed to solve the main conflict. Perseverance is a key message in the manga and Naruto epitomises this, 'getting along' is also a key message in the manga, and whether you like it or not, Naruto eventually gets along with anyone. We also know he will solve the main conflict of the story and bring peace to the ninja world, as this has been hinted at. Most of us can empathise with the character, whether we like him or not. As long as Naruto does these things as a protagonist he is fulfilling his role so can't really be considered a bad main character.