If you are willing to use a CLI solution, Duplicity is a network backup system written in python supporting, among other protocols, FTP, SCP and rsync:
Duplicity backs directories by producing encrypted tar-format volumes and uploading them to a remote or local file server. Because duplicity uses librsync, the incremental archives are space efficient and only record the parts of files that have changed since the last backup. Because duplicity uses GnuPG to encrypt and/or sign these archives, they will be safe from spying and/or modification by the server.
You will need to install GnuPG to use it (version 1 – it seems Duplicity has some issues with GnuPG 2 in Lion). If you are using a package manager, both Duplicity and GnuPG should be available through it (confirmed for homebrew). See the installation instructions here.
To run it in the background, I suggest creating a launchd task (aka LaunchAgent).