People have been saying so many good words for HTML5, but one of my main concern is how to protect the source code of my game.
essentially..
Ultimately, there is no protection of assets on the web. If you can see it in a browser, you can download it with curl. If protection of assets is a major concern for you, I don't recommend HTML and JavaScript.
You can obfuscate your code to prevent casual theft and use SSL to prevent snooping, but industrious people will still be able to access these assets in other ways.