Plain old FTP isn't very secure-- it generally sends the authentication in cleartext. If you can set up the server to use SFTP then it will be more secure, and you can also set up ssh key pairs for authentication so that you don't have to send a password when you login- when you ssh, scp, or sftp into the server, the ssh program at your end handles authentication via the keypairs. This is particularly convenient if you want to have a pair of computers talk to each other on a regular basis without human intervention. For an example, I have a web scraper that runs at home and generates database inputs from its scrapings that it uploads to the server on its own a few nights a week. I have a few of my accounts set up with ssh keys, and it's pretty convenient.
Setting up ssh keypairs isn't hard, but I don't do it often enough to have it at my fingertips-- I look it up every time. Here's an example of how to do it (first hit on google). It then depends on the general security of the machines at either end.