If you publish your project as an EXE file the SWF will be hidden but not protected. Anyone who wants to get the SWF can get it and decompile it to get at all the resources. You can make this harder but you can't make it impossible.
Third party swf2exe tools will provide more protection than a Flash EXE and will even allow you to bundle additional files and folders inside a single EXE. These tools normally add encryption and some basic protection systems to prevent casual piracy but they won't stop anyone who's really determined.
I make one of these tools (SWF Studio) see my signature for a link.
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When your swf2exe tool just HAS to work
there's only one choice... SWF Studio