Hunters are my worst nightmare as Rogue, I started off playing hunter so i faced 3 hunters last night on my rogue. First two i lost because i wasn't aggressive enough and only had no more than 2 minions on the board at a time. Turns out none of them ever had an unleash the hounds all game and must have been at the bottom of their decks.
They just burned me down with steady shot and a few spells and before i knew it i was on 10 health.
So i said next time i play a hunter i will be super aggressive and dominate the board. By turn 4 i had 4 minions on the board and he couldn't summon a minion without me killing it next go.
So at lv 4 he uses bird + hounds he gets insane card draw and i'm dead. No matter how i played i could not kill them.
deadly poison and blade flurry are you best clearance against hunter and murloc decks i find,
just use you hero power or perditions blade once and then keep it there buffed by deadly poison with a blade flurry in your hand and you can wipe the board when they try to gain board control.

. Might also try Molten Giants, but not sure how good they will be in the deck.