Every class has strengths and weaknesses.. you just need to figure out how to play against all the different classes and builds if you want to be a top pvper.
In the BGs, sure that rogue might get you stunlocked for an eternity, but how many cooldowns did he use? How long until he can do that again?
Also, you must have been alone. If you are a soft target, you need to try and avoid that.
If you only have greens or worse, your not going to last long. Make sure you have lots of stamina, no matter what class, as that will keep you alive longer.
On my 49 twink hunter, the way I counter rogues is to put up a flare and put an ice trap down in the middle of the flare and stand on it. Most rogues will avoid me or wait till I start moving.
My 70 mage would do a frost nova and blink. Then I can either sheep the rogue and run towards someone with better armor on my side or try to 1 v 1.
My 70 feral druid would switch into bear and would stand a good chance to win 1 v 1 with a rogue.
If your a priest or lock, you have fear.
If you are a warrior, you have fear and stun
I would recommend that you read up on all the classes on
www.wowwiki.com. Check out some of the wow podcasts (world of warcast, wow addons, the instance, for example).
Good luck!