Here are my opinions:
Some people hate Naruto, because:
1. It is not a very superb/great/intelligent made anime, but why are its fans hyping like it is the best one, (why even an old anime like Samurai X has better moves and story lines). In short, it is overrated.
2. Some anime fans do not like an overhyped Naruto fanbase to be a good representation of anime fans in general, (saw these guys at the arcades cosplaying naruto characters, they more look like products of a commercialized anime than real fans to me).
3. And ninja's are supposed to be cool, like Hanzo Hattori or Ibuki, Jubei Kibagami, Hiei..but why are the Naruto ninjas, a lil comedic (some whiny and noisy), sure ninjas have some light, funny moments (like in Ninja Cadets), but too much of it ruins the serious ninja mystique.
Why some people hate anime in general:
1. They think it is generally meant for kids, and some parents get uneasy when their adolescent child still watches anime with great fervor because they think he or she is becoming nerdy or geeky. Thoughts like, "he needs to socialize more", "he should be into sports", "he needs to go out more", "he will lose friends", "they might think he is weird or different and will make fun of him", come to parents minds.
2. Anime, sad to say, still has a bad reputation to the general moral public (who generalizes easily). They tend to link anime with porn, sex and violence, child abuse and child molestation, hentai (sex) games, pedophiles etc. And they usually attack anime with this aspect and shun the good ones.
3. Some people are too loud when they voice out their taste and preferences. Instead of just letting it be, they bash out on what they don't like and assert that their taste is better (some even have a racist attitude towards anime). Like a blonde sassy girl who goes "ewwww" when she sees an anime fan cosplaying as an anime character.
4. Some people are just too tired or lazy to learn or appreciate new things and stick to their cherished beliefs. These are the people who, even though they do not hate anime usually, tend to be hard to persuade when given a chance to appreciate anime that it also has its good sides.