It was rumored sometime back that Apple would allow users to use multiple iTunes account from their iPhone. However since, OS 3.0 would allow multiple accounts it becomes a piece of cake for people to share paid apps purchased on their accounts. Currently the iPhone gets locked to a single Appstore account for app downloads.
As some OS 3 beta users have seen, Apple is now planning to allow free redownload of Apps only via your iTunes installed on the local computer. Though this brings some security to developers and Apple against multiple users using an app with a single purchase, genuine users would have some inconvenience redownloading apps they already own.
Apple is planning inapp subscriptions inside App Store apps from V3.0. This might be one of the key reasons to put this check in place.