There are two general forms of FTP. The most common and oldest is FTP. In the case of FTP all files and login information is transmitted from the server to your computer and back in "Clear Text". Using this form of FTP offers some significant security holes. Anyone sniffing your network traffic will see the usernames/passwords and file transfer information in clear text.
The second form of FTP is called SFTP or secure FTP. In this case all transmissions between the client and the server are encrypted which provides the ultimate in security when communicating wiht a remote server.
SFTP is currently offered only on Linux hosted accounts.