The FTP server on Linux is deprecated, and provided only to aid migrations of legacy applications (you probably saw a warning to this effect when installing the FTP server from MAX). It does not integrate with the password configured on your target. Since the FTP protocol transfers credentials over the network in plaintext, we felt it was important to offer a more secure alternative. As noted at the end of the document you linked, on Linux targets WebDAV is the recommended file transfer mechanism. It uses a password set through NI Auth. Linux targets also support using ssh for file transfer, although there is not a VI API for that.
