Until the final version of Flex Builder 3 comes out (which should have application type as an option under new ActionScript project), there is an easy way to create an AIR application ActionScript Project with the new beta.
All you have to do is create a new Flex Project, set the Application type as AIR, and on the last screen of the new project wizard change the Main application file extension from .mxml to .as. This will then create the main .as file just like it would if you were creating a new ActionScript Project.
That’s it. Hit Debug like you would a Flex AIR application and you’re well on your way to creating an AS3-only AIR app.