One of the big problems with the introduction of iCloud, was the inability to properly segregate it from iTunes accounts on a single iOS device. With iOS 5, you had one iTunes ID, and that same ID was used for iCloud.
While in many circumstances this posed no issue, (ad there are a few inconvenient work-arounds) it did cause problems for those whose purchases were tied up to a particular iTunes ID. I'm happy to report that this is no longer a problem in iOS 6, as it now allows you to log in with separate iTunes and iCloud IDs upon first setup...