Van Gogh had angered many in Holland's large Muslim community with a controversial, sometimes explicit, film about the oppression of women under Islam.
But his brazen style and willingness to confront sensitive issues endeared him to many in Holland who pride themselves on their respect for tolerance and free speech.
One woman attending yesterday's funeral service said she fears those traditional Dutch values are going to be lost. She likened van Gogh's murder to that of another outspoken public figure -- right-wing Dutch politician Pim Fortuyn -- two years ago: "It is very sad that this is happening in the Netherlands, that you even cannot say what you think. It was the same with Pim Fortuyn. He also could not say what he thought."
Police are holding six people in connection with van Gogh's death, including the prime suspect, a 26-year-old Dutch-Moroccan citizen with alleged ties to extremist Islamic groups in Spain and Syria.
Dutch officials have vowed to crack down on Islamist violence. But authorities have been equally critical of a wave of reprisal attacks against mosques and Islamic schools in the week since van Gogh's killing.
In the most recent incident, a Muslim school in south Holland was set ablaze yesterday evening, just hours after the filmmaker's funeral. A small bomb damaged another Muslim primary school the previous day.
Dutch officials reported today that three policemen were wounded in an explosion during an antiterrorism operation in The Hague.
Authorities have given no further details about the operation, but the incident is likely to heighten fears of a rising extremist threat in the traditionally immigrant-friendly nation.
The Netherlands is a small country of just 16 million people. Of that, nearly 1 million are Muslims -- mainly immigrants from Turkey and Morocco.
And the Muslim community is growing fast. A recent government study estimated that by 2010, large Dutch cities like Amsterdam, Rotterdam, The Hague, and Utrecht will have Muslim majorities.
The Dutch have long prided themselves on a liberal immigration policy that strives to provide social benefits to all residents, Dutch and foreign alike.
It's a policy few Dutch have been willing to criticize -- until recently.
Herman Vuijsje is an Amsterdam-based sociologist who has studied ethnic relations in the Netherlands for 20 years. He says the Dutch are reluctant to be seen as intolerant of immigrants: "We had a lot of immigration from Mediterranean countries and from former colonies of Holland. And we have always been very, very tolerant and very kind toward immigrants, which is, of course, a very nice trait of Dutch culture. But we have maybe been a little bit too kind. We have been in the 1970s and '80s very, very prudent and careful with any kind of criticism towards newcomers in our country. As a matter of fact, Holland was [controlled] by very strong political taboos. And when you said, for example, that it would be a good idea for people from Turkey or Morocco to adapt to Dutch culture, you could be accused of being a racist."
But the Dutch have become stricter in their demands on new immigrants in recent years.
The center-right government has called for greater integration of immigrants, through language tests and citizenship classes. It has even stirred controversy with a recent plan to repatriate up to 26,000 failed asylum seekers.
At the same time, the government remains eager to reach out to Holland's moderate Muslim communities. Immigration Minister Rita Verdonk met with Dutch Muslim groups yesterday to discuss ways to ease escalating tensions.
Vuijsje said he is optimistic the recent wave of violence will not affect Dutch tolerance in the long-term. He said the process of integration may take many generations to perfect: "We have really, I think, as a Dutch society, done our best to bridge the gap. But it's a great gap, because many of those people come from very backward parts of North Africa or the Middle East. And it's, of course, very difficult to bridge that gap in one generation."
Some in the Muslim community say too many people are looking at growing violence in Holland purely as a matter of religious and cultural differences -- and are ignoring economic factors.
"When you look at the unemployment rates, when you look at the bigger cities -- certainly Rotterdam and Amsterdam -- the lower economic areas really have large percentages of Muslims, large percentages of immigrants," said Abdulkader Tayob, a professor of Islamic studies at the Nijmegen branch of the International Institute for the Study of Islam in the Modern World (ISIM). "So I would suspect that the socioeconomic conditions there are, in a sense, much more difficult. But there is also a very strong welfare state within the Netherlands that provides for the immigrants as it does for the local Dutch, and I think that is also a point of contention."
The rising debate over the Netherlands' immigration policy is apparent in the results of a recent Dutch TV news poll -- 47 percent of people surveyed said they felt less tolerant of Muslims since van Gogh's murder.
Another poll showed rising support for right-wing politician Geert Wilders. Wilders was recently forced out of Holland's liberal VVD party for opposing Turkey's membership in the European Union.