http://bugs.winehq.org/show_bug.cgi?id=10324
--- Comment #9 from Austin English austinenglish@gmail.com 2007-11-07 10:45:06 --- I was thinking more along the lines of locking up the system, wiping out important files (/etc, /var, /boot, etc). Not their wine prefix. It may also set some files in their home directory to be owned by root:root, which could cause confusion.
Having seen several people file bugs about lockups/other strange errors after having run wine as root/sudo was what made me think of this. While there are some instances that people need to run as root and know what they are doing, more often it's people who don't know what they're doing and think it will help for some reason.