The following fix works for me running:
OS: Linux, Ubuntu 9.04 \n \l
* Edit /etc/rc.local
* Add before "exit 0":
echo 2 > /sys/module/hid_apple/parameters/fnmode
After that, the function keys worked fine for me without pressing Fn.
For more history and related issues, see my post here: http://dancingpenguinsoflight.com/2009/01/fixing-the-function-keys-on-the-apple-keyboard-in-ubuntu