Follow these steps to setup a decent backup solution for your MT hosting (you can adapt this to any other hosting that offers SSH and RSYNC access).
First you'll want your linux box to be able to SSH into your hosting without a password using a SSH key instead.
Then, just clone the following repository somewhere in your linux box
https://github.com/PortNumber53/mt-utils
Customize the file:
mt.sh.sample
Next, make sure the variables in
0-variables.sh
match your enviroment.
Then you just need to run:
mt.sh.sample
For extra peace of mind, set it to run from a cron job.