This question has always baffled me. The Netherlands had a population of only 5,000,000 in 1907 and the Dutch East Indies had a population of about 45,000,000! How were they able to oppress them for so long without a rebellion? Even if half their army (let's say 100,000 generously) were in the Indies, how did they control 45,000,000 people? And how the heck did they even transport troops there in early years? There weren't airplanes so it must have taken a TON of ships going back and forth, right? Wouldn't that mean that ruling over the Indies would have been an absolute pain?
I know that's a lot of questions but there are some great historians here.
At the start of the Second World War, the population of the Dutch East Indies was about 60 million, of which 250000 were Europeans (mostly Dutch). The Europeans had all important economic and administrative jobs. They formed the top layer of the society. They controlled the Dutch East Indies with the support of local elites and collaborative locals who worked in the lower echelons of the administration (working for the European or local elites was preferable to working in the fields).
So there was a layered society, with Europeans at the top, local elites below that, collaborators below that, and only then the masses. The masses were kept in check by repressive by the army, police and security services. Those three consisted of no more than 75000 men - in large part locals.
In the 19th century there were several revolts which were repressed forcefully by the KNIL (Koninklijk Nederlands-Indisch Leger; 'Royal Netherlands East Indies Army'). The KNIL at first consisted solely of Dutch soldiers, but it soon would start to include locals. When the KNIL was dissolved in 1950, more than three-quarters of personel consisted of locals.
The KNIL operations usually followed the same pattern: at first the KNIL would send a small inadequate expeditionary force which would fail miserably; then they would send a larger force led by more experienced officers to 'pacify' the region. 'Pacification', of course, is an euphemism for summary executions, violence against civilians, destruction of civilian property and people's livelihoods, as well as deploying ruthless local forces from elsewhere in the archipelago (often there would be existing rivalries between the peoples of different islands or island groups).
A third factor (in addition to the layered society and the violent repression of locals) was the total control the Dutch had over the seas. The Dutch navy had about 60 warships in the East Indies. Again a sizeable part (about half) of the personel consisted of locals. The navy provided vital support to the KNIL, both in logistics and fire support. The navy also blockaded rebellious areas, preventing the rebellion from spreading to other islands. While it was relatively easy for rebels to fight a guerilla-style war against the KNIL on land, there was no way for them to defeat or even engage warships.
Sources:
Jaap de Moor, Met klewang en karabijn: militaire geschiedenis van Nederlands-Indië (1815-1949) p.199-244 Anita van Dissel, Tropenjaren, de Nederlandse zeemacht in Aziatische wateren (1816-1962) p.245-286
Both published in Bruijn & Wels (eds.), De militaire geschiedenis van Nederland 1550-2000 (Amsterdam 2003)