Editor’s note: on 7 January 2015, the office of Charlie Hebdo was attacked by gunmen. 12 people are so far reported dead, and more injured. As context, we republish this 2007 article about the magazine.

This month, the French satirical weekly Charlie Hebdo was put on trial after publishing, in its special issue of February 2006, the 12 Danish Muhammad cartoons, and a string of caricatures by well-known French artists. All were lampooning religious figures such as Jesus, Muhammad, Buddha, along with their priests, imams, rabbis - name it. The cover image by Cabu, showed, under the headline "Muhammad overwhelmed by fundamentalists", the Prophet covering his eyes with his hands and crying: "It's hard to be loved by idiots."

Charlie Hebdo is being sued for racism by the Paris Grand Mosque, the Union of Islamic Organisations of France (an association under the influence of the Muslim Brotherhood's Hani Ramadan and Yussuf al-Qaradawi) and the World Islamic League (a Saudi foundation which promotes Wahhabism). Their evidence includes three cartoons - Cabu's, the Danish drawing showing the Prophet with a "turbomb" (a bomb in his turban), and another with a religious Muslim at heaven's gates warning Islamist terrorists: "Stop, we've run out of virgins."

The background to this trial begins in September 2005, when the conservative Danish daily Jyllands-Posten published 12 cartoons depicting the Prophet in different ways. Islamist imams staged official protests throughout the world. Then all hell broke loose: burning of embassies, torching of flags, reprisal killings. In total, 140 people died in extremely violent clashes.

Europe, taken aback by such violence, seemed almost absent-minded. Its media were unusually quiet. In Britain, the historical bastion of freedom of speech, none of the national dailies published the cartoons. Jack Straw, the then foreign secretary, praised the country's editors for "considerable sensitivity" in not printing the cartoons, and attacked European publications for doing so: "The republication of these cartoons has been disrespectful and it has been wrong."

Across the Channel, France-Soir published them all, and as a result its managing editor was sacked. Soon after, Charlie Hebdo, to show solidarity, reprinted the Nordic cartoons and commissioned more drawings from its cartoonists. This act, from a satirical weekly respected for its staunch secularism (and one that even Christian fundamentalists wouldn't dream of suing for "disrespect" and "insensitivity", let alone "blasphemy"), triggered unexpected reactions.

Criticism came principally from French and foreign radical Islamists. Then from the liberal-minded left, both in France and abroad, who saw intolerance in the drawings, but not in the reaction of those who branded rational criticism acts of fascism. For instance, Sarah Joseph, editor of the British Muslim lifestyle magazine Emel, wrote in the Guardian: "Some countries that have reprinted the images - Spain, France, Italy and Germany - have a nasty history of fascism . . . Now the great shape-shifter of fascism seems to have taken on the clothes of 'freedom of speech'."

Judgment in the Charlie Hebdo trial will be given next month. Meanwhile, it has been an important way of setting the record straight. Two-dozen philosophers, politicians and writers of all convictions and nationalities have appeared in the witness box to support the magazine's case that to publish the cartoons was not racist, but a simple criticism of the political use of religion. The Islamist associations have presented only one opposition witness: a Catholic priest, Father Michel Lelong, who in the past has also supported the Holocaust denier Roger Garaudy and al-Manar, a Hezbollah satellite television channel forbidden in France because of its anti-Semitic programmes.

But what this trial has also shown is that in the past few years there has been a huge shift in our response to Islamist fanaticism. In 1989, Europeans from left and right unanimously defended Salman Rushdie against the Satanic Verses fatwa and made him an icon of freedom of speech.

Today, Europeans in general, and the left in particular, are split, with many voices accusing the Danish cartoonists of being racist provocateurs (as if minorities were, by definition, all persecuted and all worthy of universal defence) and others offering blind support to the self-proclaimed offended. As one French academic said in an interview with the national daily Libération earlier this month: "Between the political correctness of the first and the appeasement of the second, fundamentalists have all the scope they need to impose their own particular agenda."

The problem with religious fundamentalism is the same as it has always been, except our attitudes have turned upside-down. Secularists in France used to shout louder than anyone, but these days they lack vigour, apparently riddled with self-doubt. Is it fear? Religious radicals have, in inverse proportion, become more assured as they have managed to shake the universal foundations of society, and started to negotiate specific rights and legal exemptions to which their "difference" entitles them. But what difference, and where will it end?

We have to stop mistaking healthy criticism of religion for racism, and must not let discussion of immigration and security elbow out the more important debate on secularism and citizenship.

Agnès Poirier is a journalist and the author of "Touché: a Frenchwoman's take on the English" (Weidenfeld & Nicolson, £9.99)