I have a very simple Mac Cocoa app that just has a Web View that loads an HTML file with some CSS and JavaScript. I have hooked up the app delegate to this method:
- (void)applicationDidFinishLaunching:(NSNotification *)aNotification {
  NSString* filePath = [[NSBundle mainBundle] pathForResource: @"index" ofType: @"html"];
  NSURL *url = [NSURL URLWithString: filePath];
  [[self.webView mainFrame] loadHTMLString: [NSString stringWithContentsOfFile: filePath] baseURL: url];
}
The index.html file contains the following:
<html>
  <head>
    <title>Hello, World!</title>
    <link href="style.css" rel="stylesheet" type="text/css" />
    <script type="text/javascript" src="jquery.js"></script>
    <script type="text/javascript">
      jQuery(function($){
        $('h1').fadeOut()
      })
    </script>
  </head>
  <body>
    <h1>Hello, World!</h1>
  </body>
</html>
The style.css file gets loaded correctly, because I set the background to grey in that, so I know it can load other assets from the resource bundle.  The javascript code does not get executed.  If I open index.html in Safari, the Hello World h1 disappears, as expected.  Why doesn't this happen in the app in my WebView?  Do I have to do something to enable JavaScript?  The box next to JavaScript is checked in Interface Builder.
The code for this is available at http://github.com/pjb3/WebViewApp