Hype's Flexible Layout and Responsive Layout tools currently work at the scene and element levels, they do not apply to the document as a whole. Thus to use Hype's systems, you'd generally need to put all elements in a group for each scene and then turn on zoom contents. See this post in the same topic. Some folks still want to do this at the document level and thus this is still the recommended technique.
There might be some issue with your page. A simple test works for me – the $(window).resize(scaleSite); line should cause it to resize whenever the window changes.