Well, see, it is all about the amount of runs scored. If the first team scores some runs in an innings and it rains, then some sort of average is worked out, and then the second team bats to an average, or maybe a revised total, if you will. At this point, 50 overs become 35.4 and the fielding captain is able to move his field out at 6.2 overs, as opposed to 15 during a normal match. Then, what happens is the run rate is recalculated, for the possibility of further rain. When the rain does indeed arrive, the match total is further revised and the existing batsmen can count themselves lucky that they haven't been given out during the whole process.
Essentially, the Duckworth-Lewis system was devised to make it simple for captains and teams when calculating run rate required during rain affected matches. Rather than calculating the secrets of the universe, captains merely needed to grasp advanced calculus. From what I hear, a doctorate in mathematics hasn't been required in years.