I see the whole Harmonian/Zutara comparison because of the creator's disdain for the ship. But the main difference is that the Harry/Hermione became a dirty word because zealots took over the ship, forcing most of the more gentle, analytical fans to hide their preference. (Personally, I always tend to ship best friends. Zuko/Katara are something of anomaly for me... of course, they became more of a best friend ship towards the end, which totally delighted me.)

It's not to say that Zutara doesn't have its crazies. That we do. But for the most part, the analytical (dare I say "normal"?) fans keep control of the ship's helm, making it something most people don't mind being affiliated with. Actually, I think the Zutara fandom handled itself in an exemplary fashion and should be taught in school as the textbook way an OTP fandom should act. Harmonians, on the other hand, are like that saying "if you can't be a good role model, you can be a terrible example." It's almost like Zutarians looked at the Harmonians and collectively said "Yeah, we're not going THERE."

All of this is just a long winded way of saying, I don't blame you for not liking the comparison.