Securing your FTP connection to a normal FTP web server is easy so long as you have SSH access. Just dump your regular FTP sofware client and start using an application like WinSCP.
Download WinSCP and once installed follow these steps:
An SCP application like this allows you to tunnel with your SSH connection through to your FTP serv
Now when you connect you'll be presented with what looks like a normal FTP client but this time your connection is secured.
Easy to do and secure.