If you protect your self extracting zip file, you have no software protection on you actual program once it's been extracted. You must protect your program's exe file and not the self  extracting zip exe file if you want to ensure you're protected.

The correct way to protect your software is to use CopyMinder to protect your program's exe file and then create your zip file including this protected exe file, the .cm file and CMInstall.exe that are created by CopyMinder.