What are the non-anthropogenic causes of The Netherlands' low elevation?
Forming of coastline

During the last ice age, the North Sea was dry. When the ice melted sea levels slowly started to rise again and due to tides and currents
a barrier of dunes was formed along what approximately is today's coast line. This created an area of land that fell dry during ebb-tide and flooded during high tide (this can still be seen in the 'Waddenzee' in the North of the Netherlands where you can walk to some of the islands during low tide). The big rivers that flow through the Netherlands brought in more sand, slowly keeping larger parts of the land dry. 

Isostatic rebound

During the ice age, the surface of Scandinavia was pushed down. After the ice melted it started to rise again and pushed the Western and Northern part of Netherlands down. Strangely enough the Southern and Eastern parts of the Netherlands are rising, so it seems the Netherlands is tilting.
I'm not sure how large the isostatic effect has been, but we know that the North of the Netherlands is still going down with about 2cm per century (source in Dutch). 

Human influence

I know you've asked for non-anthropogenic causes, but I'm going to include this anyway because it seems human influence has had a much bigger effect on elevation than the isostatic rebound. 

In the 11th century the Dutch started to actively shape the land by building dikes and later also by using wind mills to pump out water. The Flevopolder is an example of a large part of land that has been created by the Dutch in the 1950s and 60s. When groundwater levels became lower the moors settled and started oxidizing. Researchers think that the settling and oxidation of moors today is responsible for up to 15mm decline per year (source in Dutch).

Additionally in the 16th and 17th century a lot of peat was removed from the moors and used as fuel. Peat removal created new lakes, but some of those lakes were pumped dry later and were used as farmland. Also, the weight of dikes and houses on moors still cause subsidence today in areas in the West.

In the Northeastern part of the Netherlands gas extraction has also caused local elevation drops of up to 30cm (source in Dutch) in the last 40 years.

Other sources (all in Dutch): 

http://www.geologievannederland.nl/landschap/landschapsvormen/strandwal (forming of shoreline)
http://nl.wikipedia.org/wiki/Veenpolder_(poldertype) (Dutch moors)