Sure you have more frequent IC between Bruges and Brussels and it’s shorter by about 20 min, but there are also a direct IC between Bruges and Antwerp (almost) every hour.

However, if Belgium turns out to be where you want to spend more of your time in, Brussels would make total sense if you wanted to see both Flanders and Wallonia. In that case, you could make a rough train itinerary along the line of:
Paris-Brussels (then any of the following places is a direct IC within 1-2 hours away for day trips: Bruges, Ghent, Antwerp*, Leuven, Dinant, Namur, Liège*, to name a few)-then onward to NL

*if Antwerp is your last stop in Belgium, you’re on the Rotterdam-(Schiphol)-Amsterdam route.
*If Liège is your last stop, you could take the Maastricht-Utrecht route if you don’t want to backtrack and base the NL part of the trip from Utrecht. Utrecht is a train hub and also just as easy to commute to AMS for your departure flight.