Limburg and Brabant are in the present day a lot more religious than Gelderland, as is Zeeland and a large chunk of the area North-East and East of Amersfoort.

NL is percentage wise (or rather, was) one of the countries were religion was 'on the way out', unfortunately that trend seems to have first stabilized and is now reversing. It's a pity because personally I think religion should have absolutely no place in politics or organized society, though I do believe that people should be free to practice whatever religion they want as long as it does not negatively affect others.

I last visited NL about two decades ago, and spent most of my time in a Gelderland village. I must say that I was reasonably well-tolerated as a visiting heathen ;)

As you mention, it's the religious intolerance that one finds disturbing, not religion (of any kind) itself. It is fairly rare to have one without the other these days, it would seem. The phenomenon is not limited to NL alone, I think.

That's fair but the strong Islam presence has lots of people upset to the point where I would say the Dutch (as a group, of people without religion or subscribing to some religion) are now less tolerant of (other) religion(s) than they were 20 years ago. This is a factor in the right wing extremist presence who use this to drive a wedge between people who otherwise probably would not care that much, it is clearly positioned as 'Islam against the rest'. Most notable for this is Geert Wilders, who is a complete asshole but there are others as well.

Gelderland (where my family is from) is definitely more religious than say Amsterdam, but far less than the South of Limburg or the 'Bible Belt'. At the same time, those are all various offshoots of Christianity, whereas if you were to look at Islam you will find the opposite, it is strongly represented in the big cities, where there is hardly any Christian offshoots left (and if they are they are dying).

Churches are disappearing, Mosques are rising up everywhere, and I'm not sure if the longer term will find NL with a more tolerant version of itself or if it will regress at some point.

It's not really the Islam presence that bothers people, it's specifically intolerant, militant religion that happens to be of the Muslim type. Let's be clear, nobody there is complaining about an overabundance of wise Sufi mystics.

No, but there are many more people complaining about morning calls to prayer than there ever were to complain about church bells (with the exception of Tilburg).