I think it's been explained elsewhere, but as there still seems to be confusion on this setting, I thought I'd give it a shot. As I understand it, the use percentages are not absolute references (meaning, the percentage of your battery being used by application X) but rather relative references. That is, you should interpret it as the relative percentage of the battery charge *that you have used already* that is accounted for by application X.
For example, my battery is currently at 90%, so I have used up 10% of the current charge. Phone Idle shows that it accounts for 49%... of the 10% I've used, or equivalently 4.9% of the overall battery usage.
So as the day progresses and I use up more and more of my charge doing stuff, the percentage used by, e.g., Phone Idle is going to change, sometimes quite a lot. Hope this example helps to clarify what people are seeing.