The current inability of Apple to allow for us to replace our iTunes Apple ID with our me.com address causes confusion, but not unresolvable technical difficulties.
The Confusion:
1. First of all, when a new or restored iPhone running iOS 5 asks for your Apple ID, you had best enter the email address for your iTunes Account which you have been using to make purchases. iOS 5 will automatically set up everything but mail for you using it (unless it's a me.com account). You will then have to set up mail. When you attempt to set up mail in iCloud, you will then be prompted to create a me.com account for the purpose of receiving mail via iCloud so that iCloud can sync your mail across your devices. Think about it, iCloud can't use your gmail account for mail because mail sent to you would go to gmail's servers and not iCloud's.
2. The Solution:
You need to create this me.com alternate email address to work with that same iCloud account.
You also must sign out of iMessage, and every other iCloud aspect except music and movies and iTunes Store and sign back in again except this time with your alternate Apple ID.
Then, and only then, will iCloud function as it should for you... all you who dared set up your iTunes account with a non mobile me address and made purchases therewith.
If you attempt to use your old me.com account for mail, you will either loose everything in June when Apple eliminates all MobileMe accounts, or you will follow the prompts at me.com to turn it into iCloud giving you another iCloud account complete with it's own set of calendar, contacts, email, bookmarks, etc. just to get you nice and confused.
3. What apple needs to do:
Apple needs to allow us to make our newly created me.com Alternate ID the primary email address. I understand that the downloaded music, movies etc won't work with it unless Apple attaches your your previous ID to the new ID; which, by the way, Apple does do already to some degree. I have had three or four previous AppleID's and iTunes Store has asked me for them and their passwords to enable the content, but the content was enabled without the input of previous gmail Apple IDs... I needed only to reenter my current AppleID and password and it was accepted.