Note that the Mac uses an other filessystem, HFS+ (Mac OS Extended), which follows the older HFS (Mac OS Standard).
As noted in the text, this file systems also keeps track of some file properties like the hidden flag. However, if you use "cp" for copying files, this data will not be copied. In order to also copy this HFS information, you need to use the command "CpMac", which comes with the developper package.
In particular, I've found this useful when copying application. Apple has implemented applications as special folders. When I use "cp -r" to copy an app, I end up with something that the Finder regards as a folder. When I use "CpMac -r", the Finder will recognize it as an application.