First, let's establish that the Netherlands is a car country. We have 11 million cars on a population of 17 million. On a typical day, 1 million people use public transport. Cars are the norm, not trains or bicycles.
Public transport is rarely faster, not even in the most idyllic example that you give where you go from big city to big city. The thing you conveniently forget to consider is that nobody lives near the station of city A and then also works very closely to the station of city B. It almost always includes additional travel towards A and from B. Cycling, trams, buses, multiple stops in both directions. It adds up.
To illustrate how absurdly slow public transport can be, a personal example. I used to live directly behind a train station in a mid-sized city. Doesn't get much better than that, right?
Let's explore the commute to work, some 60km away...
I have to get up early and be there some 10 mins before departure to secure somewhat of a reasonable spot. Next, I'm on route to the first big city station. This route is slow, it stops 5 times along the way as everybody needs to connect to a big hub to get where they need to be.
I arrive at the hub, where there's a 20 minute connection wait to take the train to the big city destination. This route is longer but fast, no stops along the way.
I get out and have a 10 minute connection wait for the bus to take me to the place closest to work, after which there's a 5-10 minute work.
Total commute time: 2.5 hours single way. To move 60km. And that's living behind a train station and working at one of the countries' largest employers.
What works really well in the Netherlands is living within a cycling radius from work, every other option sucks.