Depends on the source of protein, beans & pulses, nuts and yogurt I include the carb value in the meal-time calculation, if it's say chicken, turkey or fish (moderate portions of) eaten with carbs then I don't bother as it seems to have no impact on bg levels.
Protein eaten in the absence of carbs, like an omelette/scrambled eggs I have to bolus for, in fact I need as much insulin for a low-carb meal like eggs than I do for my average meals that always contains carbs, but I've seen some type 1's say that they can eat protein and not have to bolus so it just goes to prove how different we all are, the best bet is to test your postprandial bg levels and work it out from there.