Yes, the Netherlands is certainly worth 3 days (more, actually, but your trip is too short).
First...reality check: have you been honest with yourself about how many full days you have in Europe, not including the day you arrive or depart? You can not/should not count your arrival or departure days as you will be wiped out upon arrival and your departure day will be consumed with critical tasks. How many full days do you really have?
Second: Just because you have already booked your flights does not necessarily mean you can't change them. Yes, maybe there's a fee for that (maybe not, or maybe it's not a huge fee) - although maybe better flights might actually be less expensive even if you have to pay a fee to change them. You can't know this unless you check, and you do the math.
Consider this option: fly in to Paris but don't fly out of Paris (flights departing from Paris tend to be more expensive than flights from, say Amsterdam, in part due to higher taxes in Paris). So fly in to Paris, do your itinerary (maybe Paris and nearby day-trips, then Bruges, then Amsterdam, fly home from Amsterdam. That's a much more efficient routing.
This would certainly save you TIME (you wouldn't have to circle back to Paris). Remember: for most of us, time (usable days in Europe) is the commodity that is most constrained. Saving a whole day is huge. You might ultimately end up saving money, too: you skip the cost of getting back to Paris, a hotel for the last night in Paris, etc. All the things you spend money on are going to be a bit more expensive in Paris than they would be in Amsterdam. Personally, I wouldn't let a minor cost difference (either way) force me, I'd go with the itinerary/plan that allows me to maximize my usable time in Europe...and doubling back to Paris for a night at the end of your trip works against that.
Bottom line: do not ignore the option of changing to a more efficient open-jaw itinerary even now after you have flights booked. Run the numbers, take an honest look at what the cost/benefits would be, and you may be surprised.
Hope that helps.