Reason 2: the latest Handbrake version still has trouble to handle tougher copy protection like 99 titles in DVDs protected by X-project protection (from Disney, Pixar, Paramount, Sony etc), even though libdvdcss installed.
For example, Handbrake can't read the disc at all, keep crashing or repeat the first few minutes. When your Handbrake libdvdcss stops working, you will have various problems when copying protected dvds. It needs libdvdcss downloaded and installed to treat copy protections properly. Reasons 1: Handbrake version after 0.9.2 itself won't rip protected DVDs.
Can't Rip Protected DVD from Disney, Paramount with Handbrake Libdvdcss