Reading a lot about backing up over FTP, I found most people said it wasn't advisable.
This is because FTP is sending data as unencrypted binary and someone on the network can listen in and get a copy.
I found some free software, Duplicati which will not only preform an incremental backup over FTP on a schedule but also does so while encrypting. The encrypting password can be as complex or as simple as you'd like. The data it backs up is decrypted by the same software running in restore mode.
Duplicati can also backup to multiple other services:
Amazon S3, Cloudfiles, Local File, FTP, Google Docs, SkyDrive, SSH, Tahoe-LAFS and WEBDAV
Backing up over FTP seemed to compress and part-out my data at 11MB chunks.
So if you're looking for a backup solution and don't mind that this is not running from a script or able to be scheduled from windows scheduler - this is a great solution - more so than standard FTP because of the encryption option.
The program is Duplicati: http://www.duplicati.com/