The $99 is a one time fee.. but frankly even that is absurd. Why should fedora pay microsoft so that I can use my presumably IBM compatible dell PC? It is madness.
But I think the $99 is cheaper and better (given what some idiot bios developers do - remember (IIRC) one link here on HN where the bios would look for 'Microsoft Windows' or 'Red Hat Linux' on boot entries?)