I recently released an iOS and Android game using Flash. I looked around the internet for a good free program to protect the source code in my SWF and couldn't find anything so I wrote one. It's still in development and it's "use at your own risk" but it worked for me.
It's released on github. Check it out and let me know what you think.
https://github.com/Teesquared/flasturbate
I uploaded a windows binary but I recommend you follow the instructions to build it yourself if you want to give it a try.
This obfuscator works directly on the SWF file. It currently only renames symbols but it is built on a framework that could support altering bytecodes in the future.
