I agree with most people else here, Hunters arn't hated in raids, they are only hated in PvP :P.
But I personally think hunters are fantastic in raids, their misdirection, greatly helps tanks gain aggro and helps with tricky pulls like Illidari council. At high end raiding, BT and MH, they do outstanding DPS, the two hunters in my guild have 4 parts Gronnstalker(T6) each and they do some fantastic dps, and as Surivial (41 in survival, 20 in MM) They give a fantastic buff for melee which is better than Fericious inspiration. In my raids they are userally only beaten by either some rogues or a mage(Me).
I think the only beef i've heard about hunters in raid was how easy they are to play with their one button macro spam .