If you run out of mana as a prot pally, there are several possible problems, each with their own solution.
Reason one - forgetting divine plea. Divine plea is a wonderful spell, it should always be active while fighting. Glyph it, and it's doubly effective.
Reason two - not taking enough damage. This is mostly encountered in instances, and it should be rare in raids. It means you are probably overgeared for your content. There are two fixes - taking another point of spiritual attunement (which is what I did after I ran out of mana in a 10man ulduar boss fight) or pulling more mobs.
Reason three - not enough avoidance or blocked blows. This mostly occurs when soloing, and the solution is to pull more mobs. As a protection paladin, you should be able to avoid or block most to all blows, and even if you take more blows then your holy shield has charges, recount kicks in.
So pull more.