PhotoSync Companion creates the subfolders (device name and album name) in your target directory for a security reason: All photos in the iOS photo library will be named randomly with IMG_XXXX where XXXX are numbers from 0 to 9 so it can easily happen that in two different albums your have different photos with the exact same name. The same can happen if you own multiple iOS devices like an iPhone and an iPad.
If you still want to have all your photos in one folder, there is an easy trick in Mac OSX to do this: Create a smart folder. The following screenshots show you how to create a PhotoSync smart folder for a target directory 'PhotoSync' in a users 'Pictures' directory. The user has three different iOS devices and therefore photos with duplicate names: