The problem with calculating CR for classes is that not all builds are created equal.
Generally, CR = class level. However, several things can modify that.
1) NPC isn't built to the same point by as the PC's: This can be between -1 and -2 depending on how limited the NPC is.
2) NPC doesn't meet suggested wealth by level standards: This can vary from between -1 CR to the loss of up to 25% CR for non-spellcasters. Many of my NPC's don't go around in mobile arsenals, and don't have excellent gear.
3) NPC doesn't have an optimal build: This can vary from between -1 CR to the loss of up to 25% CR depending on how far from optimal you are. Many of my NPC are essentially 'noncombatants' with builds optimized for farming, business, and daily life. They take lots of skill focus feats, and put there skill points into things that help them with ordinary challenges. If one is unexpectedly defending himself from the PC's, I won't give the full XP for defeating what is ultimately not a challenge worthy of them. (On the other hand, 'defeating' them in their own field of expertise might be worth full XP.)
4) NPC is a support class (or has a support build), but doesn't have anyone to support: Many PC classes and some builds shine best when working with a group. If an NPC has this class and has to defend themselves alone, then they probably won't be worth their CR. I tend to ad hoc the equivalent of a 1 CR penalty in this case.
5) NPC has NPC class levels: This usually means 1/2 the expected CR, and in the case of commoner it means more like 1/4 the expected CR.
I takes a fair amount of work to make a level 5 humanoid as difficult of an encounter as a CR 5 monster. You shouldn't expect it to just happen and if for some reason you don't want to put in that work, whether because you are doing a low powered gritty game or because of time constraints, don't be afraid to estimate the difficulty rather than sticking to a hard and fast rule.
