I can't speak for H/Hr shippers because I ship an even more extreme pairing: SS/HG (Snape/Hermione), but I thought that H/G were the most hated pairing? I'm not 100% certain though, cuz I'm not completely in the HP fandom.
As for House/Cuddy, the hate isn't really at the ship itself, but at how poorly the writers executed it. It was stated from the get go that they were eventually going to be the canon pairing of the show, and I think everyone understood that. But the way they completely fucked up the dynamic House/Cuddy had in seasons 3 through 6, the ship and the show, was destined to crash and burn. I hate to put it this way, but I suffered through all the bad writing and all the Huddy being shoved down my throat because I believed that the show was going to eventually get better. Then they throw out season 7, and I pretty much gave up. I don't like giving up, especially not on something I've been so passionate about for years. But House/Cuddy drove me there, not even my OTP (House/Wilson) can keep me interested in the show anymore.
Slightly spoiler-y if you don't know what season 7 of House has in store for you
As for House/Cuddy, the hate isn't really at the ship itself, but at how poorly the writers executed it. It was stated from the get go that they were eventually going to be the canon pairing of the show, and I think everyone understood that. But the way they completely fucked up the dynamic House/Cuddy had in seasons 3 through 6, the ship and the show, was destined to crash and burn. I hate to put it this way, but I suffered through all the bad writing and all the Huddy being shoved down my throat because I believed that the show was going to eventually get better. Then they throw out season 7, and I pretty much gave up. I don't like giving up, especially not on something I've been so passionate about for years. But House/Cuddy drove me there, not even my OTP (House/Wilson) can keep me interested in the show anymore.