Hunter class is somehow tricky in pvp until you learn it.
They have weaknesses but they become very powerful when managed right.
In duels meaning 1 vs 1, here are some guides vs every class in wow.
Here is the first post, hunters vs rogues.
Hunter dueling rogue:
As beastmaster: the trick is to leave a dot on him, or mark. So he won’t be able to vanish. If you get stuned and nuked pop bestial wrath and frost trap him + dots/mark.
Make sure to flare on his area so you will see him. Bm vs rogues is like their anticlass/antispec.
As survival you don’t have the cc immunity, but you got other thing like entrapment which will freeze him for 4 seconds.
So you will get sapped first, wait for the rogue to start his nuke, because if you trinket right away he will extra stun you and the trinket is wasted.
Usually I was trinketing and disengage, but that’s not a very effective move vs skilled rogues. So trinket + web from the spider pet, + frost trap. If you can’t get very far use master’s call to remove the slow. But never use it as long as you are safe because it might get wasted for nothing.
Use also snake trap to get entrapment, frost trap everytime is out of cooldown. Deterrence asap when the rogue is near you and is nuking, never wait it until you have like 20-10% hp, it will get wasted.
This is a general guide, vs skilled rogues, different specs you might lose but rogues are a fun class to duel.
The difference between survival and marksman are not so many, you get 1 extra daze as marksman, more dmg, 2 detterences, but longer cooldowns on traps. Overall is better, but survival can be more fun, because you can actually have lots of interrupts, slows, etc. And a nice tip: use always scatter shot + frost trap to get entrapment. In cataclysm this will be even more important to do.