Since they were arrested in Crawley in March 2004 in connection with a potential bomb plot, the atrocity the police and security forces had been fearing took place on July 7 2005, killing 52 people and injuring 750 in central London.

Muslim students were loud in denunciation, but in the national soul-searching that followed the revelation of homegrown suicide bombers with Yorkshire accents, it is their attitudes that are being scrutinised and it is Asian-looking students with rucksacks who are most often stopped and searched at stations.

Claims that groups such as Hizb ut-Tahrir and al-Muhajiroun are recruiting idealistic students for armed jihad have been rebutted by universities in detail but are hard to prove or disprove fully. What is clear is that something very interesting has been happening on UK campuses over the past couple of years: the arrival of an articulate and assertive Muslim presence in student politics and student unions.

In universities, this has ranged from arguments about prayer rooms to furious debates about Israel and the Palestinians. As more Muslims stand for office and get involved in local unions, they are making their 300,000-strong presence felt at national level. This year, for the first time, a Muslim is standing for president of the National Union of Students.

Would the country at large have woken up to this without the trauma of July 7? Possibly not, but in the wake of the bombings, the higher education minister, Bill Rammell, embarked on a series of meetings with Muslim students around England to gauge the temperature and listen to their views. Later this month, he will be speaking publicly about what he learned.

Last week, Rammell was in a packed room at Newham College in east London at the receiving end of a barrage of questions. "From the first question people came down on him like a ton of bricks, but he handled it quite well," said Jabir Adam, 19, who is on an access course in computing.

It became apparent that resentment was directed at the media portrayal of Muslims rather than at the government - but why was the government not doing more to control the press and television?

That's not quite how it works, explained Rammell, who was heartened by the complete disavowal of Osama Bin Laden by the Newham students but shocked by the conspiracy theories in circulation, notably the idea that the 9/11 attacks were the work of the White House.

"It's very worrying when views like that are put forward," he said. That was in a different bracket to the widespread hostility to British and American foreign policy, especially in Iraq. "I disagree with some views but you can have a reasonable debate. We need to be listening but also challenging when people are saying things that are simply not true."

Waqar Chaudhary, 18, studying for a BTec National in business and hoping to go to university, quoted Michael Moore's film Fahrenheit 9/11 in favour of the conspiracy theory and said he had seen other videos suggesting involvement by the American government. "We think the whole thing goes deeper," he said darkly.

But what came across loud and clear was the resentment of Chaudhary and others at all Muslims being portrayed as terrorists because of the actions of a "few bad apples". Julie Grace, 19, who describes herself as half Muslim, half Catholic, countered: "Muslims are to blame as well; they say they are doing these things in the name of Islam."

All these students, along with Sikh student Lovejid Sarkaria, 19, who wants to become a teacher, praised the college's strict secular policy, under which there is no designated prayer room for any religion, although students can book rooms as required. This extends to having no Christmas trees or Diwali lights; the college has winter and spring breaks, not Christmas and Easter holidays.

Rammell is concerned that unreasonable demands by some Muslim students at universities - for the complete reorganisation of exams to accommodate prayers, for instance - are bound to be rejected and will then be used by extremists as evidence that the authorities are anti-Muslim. In a multicultural, but predominantly Christian country there are limits to what the state or educational institutions should do for one religion, he says, adding: "Unless we have that dialogue, there is a danger that a chasm grows up between a minority of young Muslims and society."

At Leicester University, Zakariyya Khan, president of the Islamic Society, is doing all he can to get Muslims more involved. A day of fasting in aid of the London bombings relief fund and the Pakistan earthquake appeal attracted 200 non-Muslims and raised £3,000, he says. There is no Hizb ut-Tahrir activity on campus, he insists. His friend Azim Mahomed is standing for vice-president of the Leicester students' union, a job that includes organising social events, including the boozy ones. Would he want to ban alcohol? "No, of course not," he laughs.

Wakkas Khan, president of the Federation of Student Islamic Societies (Fosis), believes that Muslim students have become more organised and engaged in dialogue. "Our voice is being heard an awful lot more. I think a lot of the hard work we did prior to July 7 showed afterwards. What could have happened was a severe backlash."

Paradoxically, anger with the British government's policies is drawing Muslims into British politics. "Our opposition to the terror laws and identity cards is very robust but I don't think in any way it is taking away from our sense of Britishness. They are making Muslims much more aware of their environment and how they can make democratic political change," says Khan.

Claims of extremism on 30 campuses made in a report by Anthony Glees, of Brunel University, were dismissed by most of the universities concerned and Rammell regards the report as "significantly overstating" the true position.

Les Ebdon, vice-chancellor of Luton University, who chaired the working group producing guidelines for universities on balancing free speech, security and religious sensitivities, believes academic freedom can only thrive in an atmosphere of respect and tolerance. "At times of tensions between communities it is essential we have universities where people can interact like that."

When Cardiff University pulped its student newspaper within hours of it printing one of the notorious Danish cartoons, Muslim students knew they were a force to be reckoned with.

Later this month, the first Muslim candidate for NUS president will appeal for votes. Pav Akhtar, currently NUS national black student officer, will be hoping for the backing of Muslim delegates, but he doesn't fit the fundamentalist stereotype. He's gay.