Book this on www.nsinternational.com. Pick a schedule that has you on a "Eurocity Direct" service.
The route will always be:
Leiden - Rotterdam - (Antwerpen - Gent) or Brussel - Brugge.
If you buy a full flex ticket you can just take any train you want on the route. Leave Leiden when you feel like it, and just hop form one train to another till you are in Brugge.
If you buy a discounted mid-flex ticket you have to take the booked train on the cross border segment.
So if you for example book Leiden - Rotterdam - Antwerpen - Gent - Brugge then you have to take the booked train on Rotterdam - Antwerpen, but for the other segments you are free to take whatever train you want.
So if you are uncomfortable with the short connection in Rotterdam just take an earlier train from Leiden to Rotterdam. There are 6 trains per hour on that route.
Antwerpen - Gent has 3 trains per hour, one of those continues to Brugge. Gent Brugge has 4 trains per hour. So on the Belgian part of the route again, do not worry. If you miss a connection you take the next train.
I have done a similar route myself on many occasions. The last couple of months I had a lot of business in the Netherlands, and would combine that with a visit to my parents, who live half way between Gent and Brugge. When you book with nsinternational you get an email with clear instructions what you can use your ticket on. They even suggest to take an earlier domestic train when connecting with an international one.