I play a lot of BGs as prot, and find I finish well up the Damage done table.
Prot gives you a LOT of stuns. Concussion Blow, Shockwave, Charge in combat, Hamstring (with the glyph), Intercept, Intimidating Shout...
These are all really useful in pvp. Add to that the spell interrupts, and spell reflect (beautiful if you time it right and several spells are flying at you at the same time) and your increased survivability and prot is looking very useful in BGs, especially for flag running in WSG and EoTS.
Having said that, a skilled player will always beat an unskilled player, regardless of spec or class.
If you can afford the respec fees, I say choose an build, get into the BGs and see what you use most and what you use least. Take this information into account when you respec and keep picking and choosing talents until you are happy. The recommended spec may not work for you, and it's far nicer to build a build that you like and are happy with than trying to adapt your play to what someone else says is the 'correct' build.
Edited, Feb 5th 2009 5:26pm by KradortheDruid