Finally, someone wrote an intelligent article regarding why you should NOT use Automatix.

No software bashing, no name calling, just straight up why Automatix is not good for your system, and how it can be fixed.

Here is an article showing all the faults with Automatix, and here is an intelligent commentary on how we can fix it, or give people easy alternatives that are safe for their systems.
I agree with this article completely. I have had issues with Automatix2 (usually right after, or during an upgrade ie: Edgy to Feisty) but still found it to be an invaluable tool for my Ubuntu installs.

If all those non-free codecs and applications were easily distributed via Synaptic or Apt-get , less people would be breaking their systems.

Look toward Ubuntu-Tutorials.com to be supplying how-tos for all of the software contained in Automatix that, although not as quick and easy as Automatix, will be properly supported, and safe to install and upgrade later on.