In a recent interview with 1UP Microsoft admitted to one of the obvious reasons you can't just pay exact change for what downloads cost on the Live Marketplace:

"The reason why we do that, the core reason, is around credit card transaction fees," said Greenberg. "If we do this in bulk, we don't have to burden the consumer with the transaction fees, or ourselves or publishers. It's about keeping infrastructure costs down and I know sometimes it's frustrating because you end up with odd points, but we don't have any plans to change that."

Transaction fees might be the "core reason" but there are plenty of other perks Microsoft gets with the Points plan. Like, say, how unused points are basically an interest-free loan. Funny how it seems to work out that you've always get a few extra points floating around in your account, hm?