1. You're basically using SSH to communicate.  SSH is encrypted, and as such can be one of the most secure methods of communication available.
2. The setup is relatively simple, as you only need a few libraries on the client computers, and an SSH server running on the remote server.
3. Permissions, users, and groups are all preserved as they would be using normal SSH.
4. You can turn off in-secure, un-encrypted FTP completely.
5. Fast access to files via your file manager application as if they were stored locally on your computer.  For Linux Gnome users, your SSHFS mounted shares will show up in Nautilus and act accordingly.

HowTo:

For Ubuntu, simply install sshfs via the package manager.  You'll then need to add your Ubuntu user account to the Fuse group so that you'll have permission to use Fuse.  To do this, go to System -> Administration -> Users and Groups.  Click on your username and click the "Properties" button.  Make sure the checkbox for "fuse" is checked and save your settings.  You may need to log out and log back in for these changes to take effect.  Now you can mount an SSH server in the directory called "remote":

sshfs landon@holleygrove.com: remote

And to disconnect:

fusermount -u remote

It's great to be able to run a command to mount an SSH server, then pop open nautlius and have all the remote files and directories listed right there just as any other files!