Think I missed out on Tumbleweed because I had a comment on my own question. Anyway, it took a month, but I found out the answer.
Global Agenda has two separate types of protection, "physical" protection, which reduces everything equally, and "melee / ranged / AoE" protection which reduces the damage type in question.
Every character in global agenda starts with 30 physical protection, and can gain more through skill choices in the balance tree.
The exact damage formula varies with the type of damage inflicted (as denoted above), which is the "X protection" used in the formula below.
(1- (Physical Protection/100)) * (1 - (X Protection/100)) = % of true damage actually received.
Because these are multiplicative, it shouldn't matter the order they are calculated, which makes 5 physical protection and 5 ranged protection identical (at reducing ranged damage, anyway).
If someone wants to edit this answer to include a nicer looking formula (I think something like this was implemented for math.stackexchange), feel free to do so and remove this sentence when you do.