Draw a graph for every user, and bill them on their average monthly bandwidth consumption. This is the easyest way
You can draw graphs directly in mtik 2.9 or if you are using 2.8 you can use mrtg or rrd on separate machine.
but it will be for a whole interface. you can use MRTG for other SNMP information and graphs, MRTG is a separate tool. you can also see all with traffic flow: http://www.mikrotik.com/docs/ros/2.9/ip/traffic-flow
normis, I would suggest something more robust and professional like using radius and a database like sql. with php they can also allow clients seeing the situation etc...