Pure HTML files can not be protected directly. There are 2 options depending on the way you are using the HTML files.
If you have a project with HTML files only, you need a tool which compresses all HTML files in one single EXE file like HTML Executable or Active E-Book Compiler, which comes with an own Viewer. Multimedia Protector now provides licensing and copy protection options. Just import the EXE file.
The HTML files are protected with the same security level like EXE files
If the protection of the flash file is the main issue and HTML files should just be invoked, import all files (including the HTML files).
In your flash code you have to add special commands:
•Extract all files from the encrypted database to a temporary folder with the command: http://FILE:testfile.html$$COPY . You have to use this command for each html file
•Start the first HTML file with the command http://FILE:default.html$$START
The HTML files are loaded into the Browser and they are not protected
For all commands see - Flash application using EXE files