They sometimes do open tollroads in certain areas of Jakarta to alleviate traffic on the regular roads, which in that case opens it up to motorbikes as well, but in general they are not allowed.
I personally would love to see big bikes being given access to tollroads, (let's say 500cc and above), however for that to happen dramatic improvements in driver and lane discipline would need to be effectively enforced. Trucks driving 30 in the fast lane really needs to be a thing of the past.
Talking about that, there is extensive CCTV coverages around all the tollroads at least in and around Jakarta, if on the spot enforcement is not feasible for whatever reason, why not just send tickets to whoever's name the car is registered to? Don't pay, can't get your registration (perhaps including other vehicles owned by the same person) renewed. It immediately is an incentive for the people to ensure that their registrations are accurate, as nobody wants to sell their car and get tickets for infractions committed by the new owner.
Fun fact on Indonesian toll roads; the few people who actually bother to get driving lessons in this country do not learn how to drive on the tollroads / highway driving as the practice cars are not allowed onto those roads either.