Just to be complete.
Run the flasher-3.5 command as root:

sudo flasher-3.5 -F <firmware file name> -f -R

when it tells you that it didn't find a device and it's waiting, plug in the USB cable into your turned off N900.

If the flasher complains that the resource is busy, reboot the computer, remove the battery from the N900, put it back in again and retry.

Usually there's no need to keep the 'u' key pressed, but you may want to do it just to be on the safe side. It just tell the N900 to boot up into flash mode.

Aniello