FTP
FTP is a plain text protocol that utilizes two connections, a control channel and a data channel. Passwords are sent in clear text, unless the server supports S/KEY.
FTP SSL (Implicit/Explicit) (also known as FTPS)
SSL provides a secure method of accessing FTP, the entire connection (including file transfers) is encrypted using SSL. This is similar to secure websites.
SFTP
The SSH File Transfer Protocol (sometimes called Secure File Transfer Protocol or SFTP) is a network protocol that provides file transfer and manipulation functionality over any reliable data stream. It is typically used with version two of the SSH protocol (TCP port 22) to provide secure file transfer.
SFTP support was recently added starting with FlashFXP v3.7 beta.