you can play either play arms or prot in bg's rather successfully. prot is a little easier to survive with without a healer, but i've noticed healers in bg's tend to follow me around more as arms. arms will do a ton of dmg compared to prot, you just might live a little longer as prot. i've held nodes in ab against 3 people many times while either waiting on help to arrive or me just killing them as prot. as arms i can't really do that, i manage to usually kill 1 or 2 before i die.
all in all, play both and see which one you like more.
here is the prot pvp spec i use: http://www.wowhead.com/?talent#LVMh0fZhoZihzrMfzidIdsGo
and here is the arms one i use for 2v2 and bg's: http://www.wowhead.com/?talent#LcbIbfIt0brRzGuioGx0s