They didn't and still don't only speak French. When Belgium colonized, they taught Dutch and French- making it one of the first African regions to be literate in European languages at the time. It seems as though French stuck around as it is more of a used language in comparison to Dutch.

Because for a long time Dutch had a secondary role in Belgium, despite being the mother tongue of the majority of the country. French was used in politics, administration, the army, even in higher education (the first completely Flemish university came into being in 1930, a century after Belgian independence). Note thas this wasn't ethnic oppression of any kind, Flemish people were very well represented in the Belgian elite, they just had to speak French as well. Most did this out of free will anyway, in the 19th century it was bon ton for the aristocracy to speak French, but even today some people from aristocratic families still fake a French accent to sound more chique.

When the Congo Freestate came into the hands of the Belgian government in 1908, the Belgian elite was still for the most part French speaking. This had to effect that the Congo became French speaking as well. When in the period from 1908 until 1960 the role of Dutch in Belgium improved, and more Flemish people moved to the Congo, many accepted the Francophone nature of the colony.

Obviously some Dutch was spoken between Flemish people and their Congolese employees/servants, and you can still find some Congolese who can speak Dutch today, but it never evolved to play a big role in Congolese society.