Because you can simply give fopen() the name/path of a file without having to do any extensive programming for interfacing with a hard drive, searching for the file, copying the file's contents into a memory buffer, etc., then you're still using a wrapper when you use PHP's file manipulation functions (granted, PHP probably lets the O/S handle some of this work, but still..).
If you're asking why there's a "file:///" wrapper, well, I can't personally answer that unless it's for compatibility/historical purposes (I know IE and the like used to reference local files with the "file:///" wrapper).