Comment 1 for bug 926401

You can make a file with your settings hardcoded into it and then make the file executable.

To get it to execute when you reboot, you would make an autostart file for the executable file you just made in usr/share/applications.

I have a blog "walkthrough"-ish, to help others with this sort of problem.

I really wanted to disable to tap-to-click.

http://thismagpie.blogspot.co.uk/2012/07/finally-how-i-permanently-disabled-tap.html

I would like to help develop a proper fix for the touchpad settings management though, as it is quite a crude fix.