A good example of this is a troll's regeneration ability. When (adequately equipped) PCs fight a troll, they typically spend a few rounds doing nonlethal damage to the troll until it's unconcious, then they burn or pour acid on it to really kill it. The troll's regeneration probably gives it an extra round or two before it gets knocked out, allowing it to do a few extra points of damage. Thus, having regeneration makes a troll worth a slightly higher CR than a similar monster without regeneration.
But if one of the PCs is a troll too, then a few minutes after the combat is over, all of his wounds are healed, without the need to use up other resources such as healing spells. For someone who's likely to get into several combats between periods of rest, that's a huge advantage. Thus, a troll PCs ECL is greater than the CR of an equivalent troll NPC.