Back in the day, malted grain wasn't made as well as it is today. This is referred to as "modification". Without going into too much detail, todays maltsters let the grains germinate a bit more, which releases more enzymes, and converts more starch to sugar.
Further, highly modified malt has pretty much already undergone a sort of "protein rest". The proteolytic enzymes in malt have already done their work. By doing a protien rest, you are just breaking down the amina acids and other good protiens that aid in yeast health and head retention.
Unless you know you are using a undermodified malt, a protein rest is not really necessary. A lot of people claim it helps in efficiency. My theory is the rest does't actually cause the boost. Its the fact that they are having to slowly heat the mash (whether direct fired, RIMS or HERMS) up to the saccharification rest. Instead of a straight infusion of hot water that will settle around 150-160, heating the mash slowly brings it up through the 130's and 140's. Starch degrading enzymes can work in temperatures as low as 130. They are just at peaki operating conditions at slightly higher temps. If you are really worried about conversion efficiency, it would be better to do a rest at 140 for 20 minutes.
Oh and G-E-R-M-A-N:
Just because a recipe calls for it, doesn't mean you have to do it. Remember, its not a recipe, it is a note of what the previous brewer did.
