Currently, Indonesia is only reachable with at least one stop (although that'll change with GA's 773's). Mind that the CGK flight stops in KUL. So KLM combines 2 large Asian cities (with a 77W IIRC).
As others commented, maybe the direct CGK flight isn't profitable. It would also mean they'd have to add another flight to KUL. So the combination of two cities seems to be the most economical if the yields don't allow for two non-stops.
KLM has indeed 5th freedom rights between KUL-CGK and SIN-DPS.