Er, I don't think Apple cares one way or the other about Handbrake... The issue is the US government, or more accurately the movie studios who are paying for their election campaigns.
There's no legal way in the US to get a DVD on to your iPod, short of buying a new digital copy, unless it came with a digital copy as mentioned previously. I suppose that plugging a DVD player into a capture card and recording it would probably be considered legal, under fair use laws.
There's nothing illegal about the actual copying of the DVD for your own use/backup. The legality ends with removing the copy protection from the disc to do so, though. Under the DMCA removing copy protection of any sort, for any reason, is illegal. Laws in other countries vary.
Anywho, just use Handbrake on movies you own and feel secure in the knowledge that you are abiding by copyright and fair use laws, but violating a really terrible law that has been used to stifle innovation and compitition as well as your fair use rights!