The struggle is no longer against religion, but within it 

And as children of the enlightenment, the bulk of the left saw religious belief itself as little more than a superstitious hangover from the pre-scientific age, preaching social deference - the rich man in his castle, the poor man at his gate - while diverting the oppressed from collective action in the here and now to the hope of justice in the afterlife. This was the background against which Spanish priests were targeted as cheerleaders of Francoite fascism in the 30s, while Soviet churches were turned into museums of atheism and Enver Hoxha decreed the outright abolition of religion in Maoist Albania in the 60s.

But many of the conditions that gave rise to earlier leftwing hostility to religion have eroded, as religion itself has declined in Europe and elsewhere. The bonds between religious institutions and ruling elites have been weakened, while the radical strands within religion - which were always present, not least in the core religious texts themselves - have grown stronger, typified by the egalitarian Christian liberation theology movement. Even the most established religious authorities have become sharply critical of the global system, challenging inequality and western military aggression. During the 1990s the Pope, who played such a central role in the rollback of communism, was one of the few international figures who could be heard speaking out against the new capitalist order. Religion cannot but find itself in conflict with the demands of an ever more voracious capitalism to dominate social and personal life, which religion has traditionally seen as its own sphere of influence.

Of course, shifts within religion have not only been in one direction: from Vatican opposition to contraception in Aids-blighted Africa, the rise of Hindu nationalism or the advance of rightwing US evangelicals, there have also been negative trends. But the loosening of the link between religion and state and economic power has allowed the secular left to work with the religious in a way that was far more difficult in the past.

It is the insurgent spirit of political Islam, however, that has brought the issue of how progressive movements should relate to religion to a head. Modern Islamism has flourished on the back of the failures of the left and secular nationalists in the Muslim world and has increasingly drawn its support from the poor and marginalised. That has had an impact on the outlook of Islamist groups that not long ago were backed by the west as conservative ballast for its client states in the Middle East. Meanwhile, Muslims find themselves at the sharpest end of conflict with the new imperial world order, from Iraq and Afghanistan to Chechnya, central Asia and Saudi Arabia - subject to invasion, occupation and western-backed tyranny unparalleled in any other part of the globe. Across western Europe, Muslims are the target of an unprecedented level of hostility and attacks, while segregated at the bottom of the social hierarchy - now forming, for example, the majority of the prison population in France.

But for showing solidarity and working with Muslim organisations - whether in the anti-war movement or in campaigns against Islamophobia - leftwing groups and politicians such as the London mayor, Ken Livingstone, are now routinely damned by liberal secularists (many of whom have been keen supporters of the war in Iraq) for "betraying the enlightenment" and making common cause with "Islamofascists", homophobes and misogynists. The pitch of these denunciations has been heightened further by the government's plan to introduce a new criminal offence of incitement to religious hatred. This measure would extend to the most vulnerable community in the country the very modest protection already offered by race hate legislation to black people, Jews, Sikhs and all religious communities in Northern Ireland. It is not a new blasphemy law; it would not lead to a ban on Monty Python's Life of Brian film; or rule out jokes about Ayatollah Khomeini's contact lenses; or cover ridicule or attacks on any religion (unlike the broader Australian legislation) - but would only outlaw incitement of hatred against people because of their faith.

Many arguments now deployed against this proposal by an unholy alliance of evangelical Christians, xenophobes, the British National Party, secular literalists and libertarians were also used against anti-racist legislation in the 60s and 70s. And none of the public opposition seems to have included the consequent logical demand that protection for Jews, Sikhs and religious people in Northern Ireland be repealed, which only underlines the noxious nature of debate about Islam in Britain.

At its most rational, opposition to protection for Muslims and other religious groups is based on the argument that whereas race is about biology, religion is a set of ideas which can be adopted or discarded at will. But in reality, just as ethnicity isn't mainly an issue of genetics, religion isn't only a question of beliefs: both are also about culture and identity. In Britain, religion has increasingly become a proxy for race. It hasn't escaped the attention of racists that many people in Britain who a generation ago would have regarded themselves as Pakistani or Bangladeshi now see themselves primarily as Muslims - nor that targeting Muslims is a way round existing race hate legislation, as well as drawing on the most poisonous prejudices and conflict of our era.

By the same token, for the secular left - which is about social justice and solidarity if it is about anything - not to have stood with British Muslims over Islamophobia or the invasions of Afghanistan and Iraq would have been the real betrayal. It is not, and has not been, in any way necessary to compromise with social conservatism over women's or gay rights, say, to have such an engagement; on the contrary, dialogue can change both sides in positive ways. But it is a chronic flaw of liberalism to fail to recognise power inequalities in social relations - and the attitude of some liberals to contemporary Islam reflects that blindness in spades.

Outright opposition to religion was important in its time. But to fetishise traditional secularism in our time is to fail to understand its changing social meaning. Like nationalism, religion can face either way, playing a progressive or reactionary role. The crucial struggle is now within religion rather than against it.