Imagine a woman – let's call her Beth – who has been an unthinking atheist all her life, just because her family and her friends are, too. One day, she decides to convert to Islam. As soon as she dons the hijab, her neighbours start to swear and spit at her in the street. A brick is thrown through her window; while she is sleeping, her car is torched.

When she speaks out publicly, the death threats come. She is a "whore" who will be "raped to death". All the other converts to Islam are receiving the same threats. Some have been beaten. Some are on the run. When they approach the police, they are wary-to-hostile. The officers ask suspiciously: what have you been doing to anger these Muslim-bashers?

If this was happening this way, it would – rightly – be a national scandal. There would be Panorama specials, front-page fury and government inquiries into Islamophobia. But it is happening – only in the reverse direction. All over Europe, there are Muslims who are exercising their right in a free society to change their religion, or to become atheists. And they are regularly being threatened, beaten and burned-out, while the police largely stand by, inert.

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Ehsan Jami is an intelligent, softly-spoken 22-year-old council member for the Dutch Labour Party. He believes there should be no compromise, ever, on the rights of women and gay people and novelists and cartoonists. He became sick of hearing self-appointed Islamist organisations claiming to speak for him when they called for the banning of books and the "right" to abuse women. So he set up the Dutch Council of Ex-Muslims. Their manifesto called for secularism – and an end to the polite toleration of Islamist intolerance. As he put it: "We want people to be free to choose who they want to be and what they want to believe in."

Ehsan was immediately threatened with death. He was kicked to the ground outside the supermarket. He was grabbed in a street with a knife put to his throat. He can't afford to be glib about the risk: he remembers the near decapitation of Theo Van Gough on the streets of Amsterdam. Yet instead of rallying to Ehsan, his party condemned him. The Dutch deputy Prime Minister, Wouter Bos, said they disapproved of an organisation that "offends Muslims and their faith".

In Britain, my friend Maryam Namazie recently set up the British Council of Ex-Muslims. She was immediately flooded with calls from frightened people who wanted to join but were too intimidated. Endless phone threats inform her that she will soon be beheaded – but she has learned that the police just aren't interested. "They have never been very helpful," she says. "They act as if it's your fault for 'provoking' these people, when in fact the Islamist movement uses threats and intimidation as a tool to silence their critics."

People raised on the honeyed multicultural platitudes that religions such as Christianity and Islam are all about love and hugging puppies will wonder why these people would take such risks to leave their faith. This week I interviewed Mina Ahadi, the founder of the German branch of the Council of Ex-Muslims, after she was named Secularist of the Year.

Mina is a warm fifty-something woman with a big laugh, and when we meet – in a house in London I can't disclose for safety reasons – she is wearing a big jumper and small, wire-rimmed glasses that make her look like any other German Hausfrau. But she has a very different story, taking me back to her childhood in rural Iran. She tells me: "As a Muslim girl, I was not allowed to do so many things. From the age of 12 onwards I was basically not allowed to leave the house. I couldn't play on the street, I couldn't mix with boys, I couldn't even do the shopping. I hated it. There was terrible violence towards the women in my community, everywhere. One of my cousins, Nahid, went into a man's house unaccompanied, and the men in my family tied her to a tree and whipped her. When I read the Koran for myself I was shocked, because many of these things are actually recommended by the Prophet Mohammed."

She soon realised she was an atheist, a view reinforced by her reading of Charles Darwin. When she went to university, the Islamists began to force a theocracy on the Iranian people. She refused to accept the mass sackings of women and the enforced veiling. She was beaten for speaking out, and had to go into hiding. One day, her husband and four of their friends were taken away. Nine months later, in another hiding place, she read that they had been executed.

She decided to seek refuge in Austria, because she read in a book that women's life expectancy there was higher than men's, "and I thought – that's my kind of country!" But she was amazed to find that even in Europe, Islamist groups were being treated as the respected spokesmen for all Muslims by politicians and journalists. Even here, the extreme wing threatened her with death for forming the International Committee Against Stoning to save women, and the police did little. On her visit to Britain, they offered her no protection at all.

If Christian fundamentalists were doing this – as they used to, and would like to again – none of us would hesitate in erupting in rage. But because Islamic fundamentalists are doing it, we feel awkward, and fall silent. The difference is the colour of their skin. There's a word for this: racism.

Women such as Mina expose a hole in the stale logic of multiculturalism. She shows that secularism is not a "Western" value: she thought of it all by herself, in a rural village in Iran. Yet the attitudes that lead to the persecution of apostates are widespread even within British Islam, because we patronisingly assume it is "their culture" and do not challenge it. Some 36 per cent of British Muslims between the ages of 18 and 24 think apostates should be murdered. The younger British Muslims are, the more they believe it – a bad sign for the future, unless we start arguing back. This isn't just kids sounding off. Some act on it: a Despatches documentary this year, Unholy War, found dozens of cases of apostates having their cars blown up, their kids threatened and even being beaten and left for dead, on British streets.

One way to keep up the pressure for this reform within Islam is to have a thriving movement of ex-Muslims. They demonstrate to ordinary Muslims that if they are appalled by the unreformed bigotry of their faith as it currently stands, there is a rich and rewarding alternative – secular humanism.

If we in Europe do not defend people like Ehsan and Maryam and Mina, who are fighting fundamentalist thugs for the basic human right to believe and say what they want, do we deserve these rights for ourselves?

j.hari@independent.co.uk