No. If reducing emissions is the goal, gas taxes are actually superior because the price is proportional the emissions you make. This tax doesn't provide a disincentive against gas guzzlers, but they already have insanely high gas taxes in Europe. To me, this seems like a supremely over-engineered means of taxation.
But if reducing congestion is also a goal, as the second sentence of the article states, a per-kilometer tax is superior. A GPS-based system can also target those who drive at peak hours and on congested roads. Given that the Netherlands is small and population-dense, they might be very interested in reducing congestion.
One problem with that is, that you can't increase the tax too much or many people will refuel across the border and evade your tax that way. After all its a small country.
They already have high fuel taxes there compared to the US. The majority of the cost of fuel is tax pretty much anywhere in Europe.