Amen. I don't understand why Apple won't let us just merge the two accounts. How hard could that be? And it would solve all these issues. I was rushing through iCloud setup last night (I have 3 iOs devices and 3 Macs) and I think I got confused on which account (MobileMe vs. iTunes) I should be using. I think I may have accidentally "locked myself out for 90 days" on at least one iOS device in the process. I can't tell. It's hard for me to keep track of. There must be some solution...
I am/was having the same problem. I ended up logging into my MobleMe/Apple ID account with iTunes and authorized my Mac to use the Apps/music. That's working great now, though I'm locked out of auto-sync and redownloading any purchese I've deleted for the next 90 days, but all is great with Wi-fi syncing! :-)
The problem I'm left with is not being able to access any of my MobileMe stuff. May iCal and book marks won't sync and I'm not sure if it's because I'm now using Lion or if it's actually MobileMe. To update any Calendars and have them sync to my iPhone, I have to go into iCloud.com. I'm still left without bookmarks though.
I'm not sure why they can't merge the two accounts, it's very frustrating for me and I'm sure thousands of other people!