Damage is directly linked to level of stupidity. Running as a normal user just what you have means to alter as a normal user at risk in most cases. Ok this is not the wisest person. Wisest person would have wine inside a selinux sandbox so damage is only what is inside the sandbox. autorun.inf is not run by wine or linux normally so those viruses don't work. Now the pure stupid run wine a root so can lose the complete system. There is no reason to run wine as root under Linux capabilities can grant wine all the network permissions it need without expanding the disk access issue. clamav scan over where wine is kinda a wise move. wineserver -k will shutdown everything that is running in wine. So blocking memory hiding viruses from windows.
