Here's what I would do.
Compile your application to a SWF file. Then encrypt the SWF using AES.
Make a "wrapper" application that loads the encrypted SWF into a ByteArray using URLLoader
Use the as3crypto library to decrypt the swf at runtime.
Once decrypted, use Loader.loadBytes to load the decrypted swf into the wrapper application.
This will make it a lot harder to get your code. Not impossible, but harder.
For AIR applications you could leave the SWF encrypted when delivering the application to the end-user. Then you could provide a registration key that contains the key used to decrypt the SWF.
Also, here is a link to an AS3 obfuscator. I am not sure how well it works though.
http://www.ambiera.com/irrfuscator/index.html
