One nice thing about hunter flag runners is aspect of the beast - they cant track you. But yes, on defense, get a person with a ton of health with a hunter and a healer, and you got a good setup. Hunters also make good offense, because by comparing your track info with the BG messages you can tell where the enemy FC is (assuming they dont have AotB up).
However, most people run around the middle of the map farming for honor. If you are in the middle, keep in mind killing stuff isn't the only thing you should do - if your team gets the flag, protect it. Concuss the enemy, or (if specced) use wyvern sting/indimidation, use charge (if you have a boar), traps, or whatever to keep the enemy from stopping your FC. Also use those abilities against the enemy FC should they get the flag.
AotC is not recommended for running, and do NOT put AotP up on your FC. If you do, and he gets dazed, it is YOUR fault for anything that happens. Basically, do what you would in a PvE (only with a lot more movement) - kill stuff and talk to your group about where they need you. You can work mid, O, or D well - you just gotta do it at the right time.