A lot of the copy-protection schemes deliberately deviate from the standards of how a DVD should be authored or written. There will be lots of hinkiness introduced into the file structure leading to all sorts of errors like file links that go nowhere, links to invalid files, etc. All the data checksum data is still there, but a lot of it is wrong because of the errors in the file structure introduced by the copy-protection.
DVD players hooked up to your televisions don't care about these inconsistencies as they are dumb devices that don't care where all the files are on a movie disc and blindly follow where the menu and cell navigation takes them. DVD drives in your PC don't care, either, till you start to do more than just play the movie. Then instead of your DVD software just blindly following the cell navigation instructions something (whether it be the OS or a file manager, or a video editing program, etc.) is trying to access, understand, and sometimes replicate the file structure of the disc. Since these copy-protection routines rely on injecting dummy files into the file structure with error-filled file links, bad data, and lots of other tricks like encryption, just using something like Nero isn't going to copy the disc.
Using a program that backs up a DVD disc that is copy-protected will usually yield you a disc that has no encryption, the file shenanigans removed, and the Region flags stripped from the disc. Since all the bad stuff has been removed the all the checksum data present is actually correct as there's a 100% valid file structure present.
I usually use Slysoft's AnyDVD as my program to remove all the nastiness from a disc. It's the only program I know that you can put a heavily protected movie in your DVD drive and then use the file manager of your choice (Explorer, Total Commander, DOpus, etc.) to just drag all the files on the disc to your hard drive & have a working copy of the movie.
