In fact, in VS, if you create a folder in the project explorer, and then create a new file in that new folder, it will automatically set the namespace for you to include that folder name. It's quite handy!
Except when you don't want it. ;) I like to use VS folders for organization, but don't want the nested namespace. In those cases it's a minor annoyance to make sure I create new files at the top project level and then move them, or change the namespace of files created directly in the folder to be consistent with the rest of the project.