Depending on team comp, individual skill, gearing, etc., Prot can do anything and everything. FC, protect FC, attack EFC, hold Orbs, attack Orb holders, teamfights, Tank Epic BG bosses, guard nodes, mine carts, and so forth.
Some players will try to confine you to certain tasks, but the reality is, we can do all of that. Take stock of your team comp in every BG lobby… If there’s a spec there that’s better for FC, communicate about it and figure out what you’re going to do instead. Just be aware that it still may fall to you to FC. I’ve been in BGBs with MWs and Pres Evokers who got locked down and someone had to grab the flag so it might as well be me 
Some will try to tell you that Tanks don’t belong in PvP at all. Don’t believe them! Ask Abombshield-grobbulus (possibly the most vocal PvP Tank advocate in the forums) if Tanks belong in PvP…