Can I use my MacBook Air to sync with two different iTunes accounts? I recently bought a MacBook Air with OS X Lion. I have an iPad (iOS 5) and my wife has a iPhone 4S. We each have our own iTunes accounts and that's the start of the problem!

I successfully opened iTunes on my new Mac and pulled all my stuff down to my Mac (movies, music, etc). I set up another account on the Mac for my wife (a non-admin account if that makes any difference) and open iTunes while logged in as her. I tried to sync up with her iTunes account without luck.  

I'm beginning to suspect that Apple only allows you to sync with one iTunes account. Is that true? It would seem crazy. The whole point of a desktop/laptop computer is to assign separate account for people and have them keep their own stuff (in this case iTunes movies and music).

Any ideas on how I can see my iTunes account from my MacBook Air user account and my wife can see her iTunes account from her user account?
Yes - make one user account for your iTunes library and a second user account for your wife. 

As far as I see, this is no problem at all having two independent user accounts on one system, each using a separate Apple ID to login to the Cloud and iTunes. I tested it on my Mac (10.8) just now using my work Apple ID under a freshly created separate user account and found it to work.

This method has worked since OS X was first developed and it's unlikely to change anytime soon. You can search here for other questions that cover how to share some or all of the songs between separate accounts, but it's always easy to combine things later than it is to start mixed and separate things later.