A 26-year-old Dutch-Moroccan has been charged with last week's murder of Theo van Gogh, who had been accused of insulting Islam.
Van Gogh is due to be cremated later on Tuesday in a ceremony to be broadcast live on television.
Hundreds of people have laid flowers, candles and notes at the spot where Van Gogh was killed. They also left cactuses, a tribute to the filmmaker's prickly nature, and bottles of beer. Dozens of people circled the site on Tuesday.
About 60 young Dutch Muslims wearing orange T-shirts reading "We won't put up with extremism any more" cycled through Amsterdam stopping at mosques to protest against the killing.
A Muslim school in Eindhoven
was attacked on Monday
They then joined a Dutch-Moroccan rally of several hundred in a park near the street where Van Gogh was killed.
"Muslims in Amsterdam are very worried and afraid but we want to say that we are part of the community and we are not going to tolerate or accept this," said Samira Abbas, a 34-year-old Dutch-Moroccan television presenter.
A wave of arson attacks has targeted at least eight mosques since the killing and a Muslim school in Eindhoven was badly damaged in a small bomb blast on Monday.
Police said they suspected the school attack was in retaliation for the murder.
Fire bombs were thrown at two churches in the central Netherlands early on Tuesday, ANP news agency reported.
"It is action, reaction. Extremism is not only Islamist but also the right wing," said Mustapha Labui, a 39-year-old Dutch-Moroccan. "It's not good to divide people into foreigners or Dutch. We have to solve these problems together."
"It is action, reaction. Extremism is not only Islamist but also the right wing"
A little-known Islamist group threatened to strike the Netherlands on Tuesday after the attacks on Muslim buildings.
"Stop the attacks on our mosques, schools and the Muslim community in Holland ... before you pay a heavy price," said the statement attributed to the Islamic Tawhid Brigades, which claimed responsibility for bombings last month in Egypt.
Dutch Immigration Minister Rita Verdonk met Muslim groups on Tuesday to discuss the mounting tension.
"The ministers and the organisations are in agreement that everything must be done to call a halt to these negative developments. They strongly reject any form of extremism from whichever side it comes," both parties said.
Van Gogh was stabbed and shot as he cycled to work in Amsterdam on Tuesday.
Van Gogh's controversial film was written by the Somali born member of parliament Ayaan Hirsi Ali and claimed that Islam encouraged violence against women.
In the film Muslim women are portrayed wearing revealing variations of customary Islamic dress through which Quranic verses written on the actresses' half-naked bodies are clearly visible.