Is there any free iOS video player that allows you to transfer and keep a folder hierarchy intact?
I'm using PlayerXtreme on my iPhone and it's keeping all level folder, you should try it ! 

I've only be using the free version so far, but it does the job (and you can get more feature by giving them an availiation on the Appstore) 


  On their website, they claim that :
  
  
  Files and Folders: Dont need to learn the app. It is almost like using Windows or Mac OSX.
  Library Organization: Organize all of your media-videos, photos, and music