*I will discuss some other anime in the text of this post so there are some spoilers, please avert your eyes if this is something you wish to avoid.*
I would say that attempting to justify the strong distaste many people have for Naruto as simple "hipster" mentality is both lazy and disengenuous. It is true that any popular franchise will have its haters and for unpopular franchises, these haters simply outnumber its fans. Given how many people have expressed reasons why they dislike Naruto, simply saying "its popular therefore they hate it" is in a way revealing that you have no true counterpoint aside from a strawman argument.
Franchises can be popular without having very much merit in the terms of literature, film or art. That is fine, this is after all the mass media which focuses on entertainment. Its end goal is not to create works of art but to service the needs of its audience. The problem I believe is that Naruto's fandom contains elements which tend to push it as the best thing to hit anime since Tezuka picked up a pen. Its not.
Throughout the thread there are many valid arguments made. That the story drags or interesting characters fall by the wayside. We've seen the former many times such as the Namek Arc of Dragonball Z. DGZ is another old favourite that sometimes contained episodes that comprized mainly of muscular men grunting at each other for the better part of half-an-hour. Believe you me its sometimes difficult to explain to Junior why Daddy ever watched such a show. After a certain period of time, just about every character that was not capable of becoming a super saiyajin was essentially cannon fodder or plot device. Death Note also entered into a downward spiral when L died and never truly recovered its former heights. In either case when the relationship between the characters take a dive, so does the quality of the work. Not everyone will identify with the main characters and the auxillary cast keeps us both engaged and entertained. Cutting them out (or in the case of Naruto, cutting them UP) is not always a good thing.
In the case of Naruto, I personally do not enjoy the antics of the titular character. It may seem endearing to some and others can identify with the teenage angst that is pretty much the early characterization of Naruto. That he attempts to transcend his birth and become a person that others would respect is a noble and worthwhile goal. And I believe that this is where a lot of people get engaged in the story as plenty of people can empathize with such a motivation. That he is an annoying teenager makes him more authentic; adults know that teenagers can be annoying, having one that acts like a real teenager is sometimes refreshing. Bleach's Ichigo is a noble person who helps the helpless, protects his friends and pretty much saves the day. You may as well have tattooed "Hero" on his forehead since his characterization hinges on it. It may be ironic but as much as young Naruto annoyed me, I enjoyed him more than the Ninja Jesus that has taken his place. At least Avatar the Last Airbender's Aang grew into the role and that was the entire point of his narrative. Naruto went from "Sasuke I will save you!" to the Messiah with not all that much prelude.
The character of Sasuke however has proved divisive; he is popular with a portion of the fandom but is loathed by another. He is, in many ways, the antithesis of Naruto. An in-born genius whose goals are ultimately destructive and, some would argue, self-destructive. He is a wish-fulfillment character and Superman has been a beloved character for decades so I believe that speaks of the degree of staying power that such characters can have. However, Sasuke is, charitably, not a nice person. Essentially we are watching a very psychologically damaged young man with incredible power seasoned with burgeoning sociopathy. Its little wonder that more than a few people do not enjoy his place as secondary (or even primary) protagonist/antagonist. For some the fact that he is really, really pretty absolves Sasuke of everything up to and including murder. For others... not so much.
Add onto this the aforementioned loss of supporting cast and I think you can catch a glimpse of why Naruto is not as well liked as it can be. Overall I believe that it is a decent work that jumps up to a good level of quality when its on song. However the hate surrounding it comes from a combination of frustration, dashed hopes and obnoxious elements of the fanbase. It think its likely the third that gives Naruto the kind of visibility that provokes an extreme antipathy that outstrips the rest of its cohort in the current Shonen trinity, Bleach and One Piece. The latter two have their own hatedom but rarely do we see the sheer numbers or depth of feeling as the Naruto hatedom. What seperates them is the number of militant fans who, honestly, give the rest of them a bad name. By no means are Naruto fans obnoxious but they do harbour in their ranks individuals who are and its contributing to their favourite anime becoming a byword for over-hyped drivel. Ironic and sad really.