Somehow, Saudi Arabia was left off the most recent list of allies in our war on terrorism. Is this to send them a message, or is it a final recognition of the reality--that they're not only not our allies, they're the enemy?

If you are quoting the article I think you are. There was a mention that some of the states left off the list of allies were done so at the request of the governments involved.

Kuwait is not on that allies list, for example, and it is dead certain to support US forces in an invasion and overthrow of Saddam Hussein.