I believe the idea behind it is to provide ranking points, like you get in Tennis or Golf. Each series is given a weighting dependant on the class of the competion and the drivers score points on a rolling 52 week basis. ie the current rankings should cover Sept '99 to Aug 2000.
As I recall the top 'weighted' series are F1, CART and NASCAR, but as CART and NASCAR are truely competetive, in that you get a lot of different winners, its usually an F1 driver on top. I don't think that the quality of machinery driven in a given series is taken into account in the calculation of the points.