Bear with me. This is going to be long and, in all likelihood, analytical. However, it is majorly unbiased, so I encourage you to read.
In general, I have no great love for JRPG's. This isn't to say that I have any great hatred for them, either. On the contrary, I've found several that have been more than enjoyable for me (Chrono Trigger, Final Fantasy 4/6/8/10, Kingdom Hearts I/II, The World Ends With You, Drakengard [what a great ad for square], and essentially the entire Tales series of games). I am also a huge fan of Western RPG's, too (Baldur's Gate, the Fallout series, Elder Scrolls, Dragon Age, etc.). They all have their fair share of blessings and their fair share of faults. Linear Gameplay vs. customization is really the major line between them. JRPG's have a totally linear story (aside from the ever-popular side quest, but those don't really count, since eventually you're drawn back to that one dungeon/city/tower) while WRPG's possess a more open-ended world, allowing for much more exploration and depth concerning the world itself (which, unfortunately, can lead to an absence of side quests and deep story elements. I'm looking at you, Dragon Age).
One poster used the term "Rail Playing Game." While I don't like the nasty things this term insinuates, as the rail shooter is, usually, something laughed at, it's a rather accurate way to describe them. I'm mainly a tabletop RPG player, so that's where I get my ideas as to what constitutes a Role Playing Game, and JRPG's are not. I don't play a JRPG for an innovative gaming experience or D&D-esque character building. I play it to find out what's going to happen next in the story. It's like reading a book or watching a movie, only with a little more interactivity.
WRPG's are what I play when I want to define a character, when I want to explore the world. I'm primarily a GM (game master) when I tabletop game (I'm D&D turned Pathfinder, for anyone who cares), so I don't ever really get the chance to sit in the character's position. I'm usually the story-teller, so a game like Baldur's Gate or Dragon Age that allows me to put myself in the driver's seat (for the players really are the drivers in a tabletop game, as much as over-zealous GMs might disagree) and allows me to make the choices. It allows me the illusion of control over the game. And that's all I really ask is the illusion of control.
The only JRPG that ever gave me that illusion of control was Golden Sun. It might be said that you never really made any decisions. But Isaac, as a truly silent protagonist, really thought whatever you wanted him to think. His motivations for the quest at hand were your motivations, even if the quest itself was just part of the linear storyline. For this reason and the fact that it was able to pull off a truly epic and immersive story at the same time, I might say that Golden Sun was one of the greatest, if not the greatest JRPG I've ever played. This, I think, is one of the reasons people despise JRPG's so. They want that illusion of control that even a silent protagonist provides. However, in the majority of JRPGs, you don't get that illusion. Your main character has dialogue, and through that dialogue, their motivations are made clear and quite separate from your own. Even if they're the same, they're not yours. (Note: It might be said that Chrono Trigger also has this "silent protagonist" syndrome. However, I didn't nearly have as much fun/of an immersive experience with that game)
Moving onto this "hate" that people have for JRPG's. There are several people who don't like turn-based combat, plenty who don't like the stories, plenty who hate it for androgynous characters, plenty who hate it for any number of game-based reasons. However, I believe that the majority of hate that JRPG's get is based on one reason: the Otaku culture.
There are plenty who despise this culture. I feel a certain amount of "racism" toward it, myself. They cannot stand the immature "aura" that groups of Otaku quite often emit. And before you bash me for that statement, I did use the qualifier "often." While that may sound like a cop-out, it's really not. It was put best in Men in Black: "A person is smart. But people are dumb, panicky animals and you know it." The same applies to Otaku. I'm sure that any one member of a group is very mature on their own. However, in the group, the group mind does take over, and in my experience(which is considerable), discussions in a group of Otaku are not about deep, powerful issues so much as they're about what Phoenix Wright's attacks would be if he were in Brawl.
Back to the main issue (I ramble), this general hatred of the Otaku culture causes a hatred of anything related to it. Someone who has met particularly obnoxious Otakus will, most likely, begin avoiding anything to do with it. They'll shun anime like the plague, manga like it's cancer, and the JRPG like it's AIDS. Thus, we get the "haters" that can't back up their arguments with anything other than what Yahtzee says (sorry to Yahtzee, but it's true) simply because they haven't played them and will never play them due to their bad experience with Otaku culture.
I've got more concerning Otaku culture. But it doesn't really belong in this thread. Maybe I'll make my own for it. I wrote a 15 page essay for my Comp 102 class on the hatred and flak that D&D and its players got in the 80's and 90's. Otakus, in recent years, have been kind of getting the same sort of rep (minus the demon-worshipping bit).
Thanks for sticking with me. Hopefully I wasn't too offensive to anyone.