Automatically sync directories via FTP during off hours?

"I think you are looking for something like MozyHome

How It Works

Sign up for an account.
Create a MozyHome user account which will allow you to download MozyHome software. It's quick, easy, and our step-by-step instructions will guide you through the process.
Download and install software.
MozyHome downloads in just seconds, and the installation is simple and fast.
Select files to be backed up.
Simply check the boxes next to the backup sets, or types of files you want to back up, and MozyHome does the rest. In addition to selecting files by backup sets, you also have the option of selecting specific files and directories.

URL: mozy.com/home

or try dropbox

Unlike other programs, Dropbox doesn't have a complicated interface to learn. It's built right into your desktop! Here's how to get started:

Step 1: Drag and drop any file or folder into your Dropbox folder.

Step 2: Once your file/folder is inside your Dropbox folder, the program immediately starts syncing it to our secure servers. Once this has finished, the file's icon is marked with a green check. Your file is now safely backed up online and also accessible from the Dropbox website. (http://www.getdropbox.com)

Step 3: Install Dropbox (http://www.getdropbox.com/install) on other computers you use, and they'll also receive a copy of the files you've put in your Dropbox.

That's it! Now that Dropbox is watching your file, any changes you make will sync up instantly and automatically. This gives you the freedom to work on any computer you choose. For more help adding files to Dropbox, see here: www.getdropbox.com/help/90

URL : www.dropbox.com"

"You may like SuperFlexible, which can also backup onto 'the cloud', on the Amazon S3 servers.

BTW, using plain FTP is very unsecure and should not be done with any personal or company data."