FTP is not establishing a secure connection, so what you have is no different from before. Get a distribution of ssl-using tools and use them. OpanSSH comes with ssh which replaces telnet, scp replacing rcp, and sftp for ftp. On Win32, I hear good things about Putty, but I've never used it.

Once you have the tools, use the accompanying utilities to make yourself a key pair, and install the public key in ~/.ssh/ on the remote server, as directed in the docs.

After Compline,
Zaxo