Its to do with the energy density of foods - its the same reason that rice krispies aren't free even though rice is. You could easily eat a lot more calories from rice cakes than you could from plain old cooked rice. Plus, you would usually eat boiled rice as part of a meal, and therefore the rest of your meal would limit the amount of rice you eat, whereas you usually eat rice cakes as snacks, and therefore don't get the natural limiting factor of all the superfree food that you get in a meal.
The fact they are marmite flavoured is incidental - it doesn't really matter what flavour they are they will have syns.