It's not different than most websites. Most websites cannot be moved from a root to a sub folder without incurring some display problems. This includes PHP, ASP.NET, Ruby, etc.
This is because absolute paths were used for the resources in the header and footer for CSS, images, and
JS. For example most of the resources look look like this:
http://www.yourdomain.com/Content/scripts/global.js
when you moved everything to a sub folder those paths didn't change to reflect your sub folder.
The difference that I think you mean is why do ASP.NET Webforms allow me to do this. That is because WebForms manage the paths of the resources for you, and adjust those accordingly.