Simply put: because at that time (1885 for the Congo Free State, 1908 for the Belgian Congo) Dutch and French were not on the same footing in Belgium.

French, until well into the 20th century, was considered the elite language, to be used for higher education, administration, laws and politics. Dutch was viewed by a lot of the bourgeoisie as a "peasant" language. Just to show how long this went on: there was no official Dutch version of the constitution until 1967. That's seven years AFTER Congo became independent.

To put it on a very broad timeframe until World War II

• Dutch only became an official language in 1898 with the equality law. (http://www.ejustice.just.fgov.be/eli/loi/1898/04/18/1898041850/justel). This however did not mean that Dutch suddenly had the same standing as French. French was still regarded as the main language of Belgium with Dutch being a secondary language only in Flanders.
• During the next few years more Flemish demands (the University of Ghent offering courses in Dutch, Dutch-speaking Army regiments, the recognition of Flanders as a Dutch-speaking region) were either ignored or shelved
• World War I started with most of Belgium occupied. The German occupiers tried to exploit the Flemish resentment by a Flamenpolitik. Two of the best examples of this were: The University of Ghent became Dutch speaking and Belgium was divided into two administrative regions: Flanders and Wallonia
• Meanwhile at the front a growing number of Flemish soldiers, who were typically low ranked as officers were required to speak French (but not Dutch), started/joined the Frontbeweging. This because they felt that Flemish soldiers were not treated on equal footing as French-speaking soldiers. For instance: a lot of the documents, even epitaphs on crosses were only in French.

I can go on about the Frontbeweging for another 50 pages but important to remember is that at the end of the war they failed to keep their support and grow into a real political movement. In part because most of their frontline supporters just wanted to go home after 4 years of war and because the German "Flamenpolitik" and subsequent collaboration had given anti-Flemish forces ammunition to call the Flemish movement traitorous and anti-Belgium.

As a result only some minor adjustments were made but nothing significantly changed for the Dutch-speaking population of Belgium. That wouldn't happen until the rise of fascism and the VNV (Flemish National Union).

By that time Congo had already been a colony ruled by a French-speaking burocracy for over 40 years.