DVD to iPod minus the aggravation
Granted, Handbrake's developers state that the best way to use their program is by supplying it with unprotected video files to begin with. And that's the trick.
The answer is the new beta of MacTheRipper (3.0), which offers a workaround for this new technique. Once you've nabbed a rip using MacTheRipper, Handbrake will grab the ripped video files from your hard disk and package them into a MPEG-4 or AAC format that's perfect for your video iPod, iPhone, or for on-the-go viewing on your laptop. Now MacTheRipper is freeware, but you'll need to contribute to the developers' coffers if you want to get the 3.0 beta at this point. When you do, let 'em know Download Squad sent you.