According to this, the VOC only controlled some ports, cities (like Batavia/Jakarta) and its surrounding. Yet, it seems to be a very successful corporation, mostly benefiting from the natural resources of what is now Indonesia. How did they become so rich without controlling most of the territories? Why couldn't the locals make that much themselves?
To fill out JK's answer: the VOC directly controlled very little except the shipping routes to Amsterdam (and a few other Dutch ports, but the majority of goods arrived at Amsterdam).
Indirectly, through deals and influence at the local courts of the rulers of the islands, they controlled far more. By supplying those rulers with weapons, advisors, European luxury goods, etc. etc. they effectively had exclusive trade agreements for most everything that left the islands for the outside world. This was of course later turned into direct control, with the local rulers becoming ever more figureheads for the Dutch governors and their governments, until eventually the Dutch East Indies became a full colony with a permanent Dutch controlled civil service.
As the Dutch fleet in the area was also the most powerful in the area (more powerful than even the British for a long time, in fact during the early stages of WW2 the combined Dutch/British/American fleet in the area was under Dutch command because they had the largest contingent of ships and aircraft) their was little that competitors could do to break the VOC's trade monopoly (the Portuguese tried, and later succeeded by subterfuge as they smuggled nutmeg and other seeds out of the Dutch East Indies to their own colonies, causing in years following the prices of those commodities to crash in Europe as supply overwhelmed demand).
Te VOC was not interested in control of people or land, but trade. For example nutmeg; the dutch burned every bit of it except on an island of 1 square km so they could control all of it. IIRC the value would go from 1 in Indonesia to 50000 in Amsterdam. The VOC was the single most profitable company in history (according to my prof.). A journey would take a total of three years, and was very dangerous, but every ship that came back would earn it's cost back multiple times. Also the VOC aggressively took in the local market and forbade the locals from selling anything themselves, all inter-Asian trade was to go by the VOC.
Short answer: Indonesia is a very concentrated country in terms of the disposition of its population.
Jakarta is a port city and capital located on the island of Java, one of the smaller of Indonesia's main (top five or six) islands, but which has over half of Indonesia's population. Add neighboring Sumatra, and you have three quarters of the country's population on less than a third of its land area. Located strategically at the west end of Java next to Sumatra, Jakarta thus serves a population of nearly 200 million, more than any country in the world except China, India, and the United States. While the absolute numbers were different in colonial times, the relative order of magnitude hasn't changed that much.
It was a case of "all roads lead to Rome." An Indonesian who wanted to sell to Europe would take his goods to Jakarta and sell it to the VOC. Ditto for a European who wanted to sell to Indonesia. Under the circumstances, controlling the import-export trade of Jakarta was tantamount to controlling the foreign trade of Indonesia, then and now, one of the most populous countries in the world.