Essentially this is a question about the status of Dutch in Belgium itself.

When Belgium was founded freedom of language was inscribed into the constitution. That however didn't mean the languages were equal. For all of the 19th century and the first half of the 20th, Dutch was essentially a second rate language. The reasons for this are fairly mundane: the European elite in general spoke French, even more so for the Belgian elite where the Flemish upper class often spoke French despite being historically and ethnically Flemish; all higher education was in French; the wealthiest part of the country was in Wallonia and French had the same lingua franca-status English has now. French was thought of as upper class, cosmopolitan and even civilized compared to "rural and coarse" Dutch. Some even went as far as to consider Flemings a lesser race (this being the era of Blumenbach and his ilk) though that never garnered much traction.

Not only was French the language of the elite, more relevant for this question is that it was also the language of administration and governance. All government communication was in French, the judicial system was in French and the entire state apparatus used French. (to illustrate, the Dutch version of the Belgian constitution only became legally valid in 1967)

So when Belgian colonists came to Congo, they did so under the auspices of a francophone king, as citizens of a francophone government (ignoring for the moment the special status of Congo as Leopold II's "private" colony until 1908), controlled by a francophone administration in a world that used French as a lingua franca; and most of them came from the educated and wealthy - francophone - social classes. What society they set up in Congo heavily favoured French as well; just like in Belgium higher education was in French and there was a sort of linguistic segregation, the French-speaking colonists had the better jobs and houses, and the Dutch speaking ones suffered similar discrimination as they did in Belgium. Not that there were a lot of Dutch speaking colonists, the vast majority were francophone.

The Flemish movement after WWI did try to address this, attempts were made to challenge the French dominance and send more Flemish colonists. But ultimately to no avail, and until Congo's independence French was the language of those in charge. There's some interesting stuff concerning the Flemish movement and their emancipation struggle, contrasted with the Belgian role in the Congo but it's not my area unfortunately.

Source: Bambi Ceuppens' "Congo made in Flanders?"

It actually goes in great detail on the Flemish movement in Congo but I've only just acquired the book so my apologies if this is a rather simple answer.