The following correction was printed in the Observer's For the record column, Sunday 5 September 2010

The article below said: "It took until the late 1940s for a Catholic – Richard Stokes – to be appointed a government minister", but a Catholic convert, the Marquess of Ripon, served in 1886 as first lord of the Admiralty in Gladstone's third and fourth governments and in the cabinets of the successive Liberal prime ministers. Henry Matthews was home secretary from 1886 to 1892 and the Duke of Norfolk was postmaster-general 1895-1900. The Labour cabinet included John Wheatley as minister of health in 1924. And Richard Stokes actually served as minister of works from 1950 to 1951.

As Benedict XVI's arrival in Britain on 16 September draws ever closer, the list of those attacking him grows longer. First, there were militant atheists such as Christopher Hitchens and Richard Dawkins, who want the pope to be arrested for what they allege is his complicity in covering up the crimes of paedophile priests. Then a Foreign Office mandarin, in a leaked memo, took a pop at papal teaching and suggested Benedict should be asked to visit an abortion clinic or launch his own brand of condoms.

There has also been a growing chorus of complaint about why British taxpayers, in this age of austerity, should pay £12m towards the cost of the pope's three days in Britain. And now Penguin is to publish, on the eve of the visit, The Case of the Pope, a polemical tract by a leading human rights barrister, Geoffrey Robertson QC, arguing that Benedict should be stripped by the international community of his status as "the one man left in the world who is above the law".

Confronted by this assault on their spiritual leader, Britain's six million Catholics are under scrutiny as never before – and many seem to be uncomfortable in the spotlight. That, at least, is one explanation being offered for their reluctance either to cough up their required £7m contribution for the visit, or take up the tickets that have been sent to their parishes by organisers, but which are now being returned unclaimed, despite the announcement last week that Susan Boyle, the overnight singing sensation from Britain's Got Talent, will serenade Benedict in Glasgow.

To stand up publicly and be counted as a Catholic in Britain right now can be to invite a tirade, as I found when I accepted an invitation from the Oxford literary festival to defend the role of faith schools against an author who had published a book questioning them.

Five minutes before we went on stage, the organisers announced to me that philosopher AC Grayling had kindly agreed to chair the event. That is AC Grayling, the second-best known militant atheist in the country, hardly your typical neutral chair. And then as we were walking into the hall, Grayling informed me that "Richard" had agreed to make a contribution – Richard Dawkins, that is, the best-known atheist in the country on account of his diatribe against religion, The God Delusion. An even playing field? Of course not, and had a representative of any other minority been set up in such a fashion the entire literary world would have been signing petitions. But I was defending the Catholic church, so normal rules didn't apply.

There is, granted, much that many mass-goers feel ashamed about in their church's recent conduct. The number of Catholic priests in this country accused of sexually abusing children may stand at 0.4% of the total – accused, that is, not convicted – but the revelation that they had so degraded a vocation that Catholics have always been taught to hold in the highest esteem came as a profound shock.

As did the efforts of bishops worldwide, up to and including the future Pope Benedict, according to some unsubstantiated but well-publicised allegations, in covering up these crimes. Cardinal Cormac Murphy-O'Connor, leader of the Catholic Church in England and Wales until 2009, had, while a bishop in the 1980s, moved a known paedophile priest from one posting to another where he continued to prey on children.

So there are immediate reasons why British Catholics are cautious about launching an all-points defence of their church in the current climate when confronted by the new breed of abrasive secularists. But the vacuum left by that reluctance to hit back is now being mercilessly exploited. Much of the current wave of criticism of faith schools, for example, has been directed almost exclusively at Catholic educational establishments, with the charge being laid that they practise religious indoctrination out of the public purse and flout government admissions guidelines.

There is a debate by proxy going on here. The real concern of many who attack faith schools appears to be the granting of voluntary-aided status (state funding) to Muslim schools, where there is some evidence that it is not always being spent in the cause of toleration and mutual respect. But the critics are nervous of being seen to attack Islam, lest they are labelled bigots, but Catholic schools – where the evidence of abuse is, according to the government's own inspectors, slight – apparently provide a useful and risk-free alternative.

In a recent interview, composer and devout Catholic James MacMillan, who has produced a new setting of the mass to mark the papal visit, labelled the current wave of anti-Catholicism as "the new antisemitism of the liberal intellectual". So why don't other Catholics follow MacMillan's example and speak up more often in their own defence?

One reason is history, the lingering sense that Catholics are here in Britain "on tolerance" and so attacks are something to be endured – or offered up, as my Christian Brother teachers used to tell us. For almost three centuries after Henry VIII's break with Rome, those who remained Catholic in Britain faced something much worse than verbal attacks. It was a period of intense persecution with penal laws, Catholics barred from holding public office and even, at times, owning land, and the prospect of imprisonment, torture and execution if caught attending mass. It was only in 1829 that the Catholic Relief Act allowed Catholics once more to vote and sit in parliament, and, even then, it took until the late 1940s for a Catholic – Richard Stokes – to be appointed a government minister.

The fact that today it is scarcely noticed whether MPs or ministers are Catholics is a mark of how far tolerance and integration have progressed, but the experience of persecution has left its mark in a church that instinctively keeps a low profile and shrugs off criticisms rather than confronts them.

While they may feel different from their fellow citizens, most Catholics would dismiss the idea that they face much by way of prejudice because of their beliefs – or any more prejudice than other people of faith in secular times. "It is really not something that I have ever experienced," says author Mary Kenny, master of The Keys, the Catholic writers' guild, "except from old-style 70s feminists who will say, 'Oh you're so Catholic, you're so rightwing'."

However, the debate about a residual anti-Catholic prejudice has been more animated in Scotland. James MacMillan has spoken publicly about how discrimination against Catholics is still alive and kicking there, referring to it at the Edinburgh festival as "Scotland's shame". And it is from Scotland, too, that most of the pressure has come for a symbolic repeal of the final piece of official post-Reformation discrimination against Catholics – the 1701 Act of Settlement, which bars them from the throne. Cardinal Keith O'Brien, leader of the Scottish Catholic church, has labelled this piece of legislation "state-sponsored sectarianism" that has no place in a multicultural, tolerant society.

The difference between the experiences of Kenny and MacMillan, both high-profile Catholics living in Britain, is instructive and points to some of the internal tensions in British Catholicism that make it less effective in tackling its external critics.

There seem to be almost as many forms of Catholicism here as there are Catholics. There is, in simple terms, no single, shared template for the British Catholics who will be greeting Pope Benedict next month.

For a start, the Vatican regards Britain as two separate entities, for reasons that date back to the time when England and Scotland were independent kingdoms. So the pope will be greeted on his arrival in Edinburgh by Cardinal O'Brien as the leader of an 800,000-strong Scottish Catholic church, and in London by Archbishop Vincent Nichols as head of the Catholic church in England and Wales, which numbers 5.2 million.

This figure – produced by an Ipsos Mori poll in 2009 – shows a steep increase from the 4.2 million (or 8% of the population) reported by the 2001 census and is usually ascribed to the influx in recent years of immigrants from the Catholic countries of eastern Europe. Even vocations to the priesthood are currently showing a gentle upturn, after decades in freefall, with 150 men now in seminaries and another 40 expected to join them in September.

How to define membership in the context of Catholicism is equally problematic. In theory, for example, all Catholics are "obliged", according to the Catechism (or rule book), to attend mass each Sunday. Yet of the 6 million British Catholics, roughly only one in five is in the pews every weekend. This high rate of setting aside official teaching – in a church that is still perceived by its secular critics as authoritarian and controlling – reveals the à la carte approach of the current generation of believers to what were once the non-negotiables of the faith. A church that likes to present itself as unchanging in the face of the modern world is, in fact, changing pretty rapidly.

And then there is the wide divergence in parish life around Britain. I have been spending August in Norfolk, where our local Catholic parish is 100% white and quietly prosperous, and where my wife and I, in our late 40s, still qualify as "that nice young couple".

By contrast, for the rest of year we attend a vibrant, multi-ethnic Catholic parish in west London with a predominantly young congregation that combines Filipinos, Ethiopians, Chinese, Europeans of every description and those like the wonderful Queenie, 91, with her nine children and countless great-grandchildren, who represent a still powerful ethnic Irish contingent.

Similarly difficult is any attempt to neatly divide British Catholics into factions. Yes, at the extremes there are organisations (usually tiny, but articulate) that bang the drum for their particular causes. Cwo (pronounced "Quo"), for instance, supports female priests and plans to mark the pope's visit to London with advertisements on buses shouting "Ordain Women".

At the other end of the spectrum, Pro Ecclesia et Pontifice offers "an orthodox response to the crisis in the church" but struggles to muster more than a dozen protesters for its vigil in London where, to its fury but with the blessing of the bishops, a mass is said each week for the gay and lesbian Catholic community.

Such demarcations tend to go over the heads of most British mass-goers, who seem effortlessly to combine so-called "traditionalist" and "liberal" approaches to their faith. "We have always been a broad church with 57 varieties," says Mary Kenny, "which is why we need the magisterium [teaching authority of the pope] to pull us together."

It is a point echoed by Bishop Kieran Conry of Arundel and Brighton. "I am often told by those Catholics who dislike the way our church operates in this country that they are the 'silent majority', denied a voice by people like me in the hierarchy," he says. "The reality is that they are a very small minority. Pope Benedict is coming to a country where Catholicism is unusually stable, cohesive and vibrant enough in the current overall context of decline of interest in the church in western Europe. Indeed, I think he may well be relieved to be coming to a place where, unlike some of his other recent trips, there are no big problems for him to sort out."

Well, that might be going a bit far. Catherine Pepinster, editor of the influential Catholic weekly the Tablet, offers a more nuanced assessment. "If you developed an interest in British Catholicism by reading the various 'Catholic' blogs that have sprung up in recent years, you would conclude that we are in the midst of vicious cultural wars," she says. "But when you get to the parishes, nobody seems to be at anyone else's throat. The idea that there is a crisis is mistaken, though the church should nevertheless be asking itself why there are so many lapsed Catholics."

One blogger popular with more conservative Catholics is writer and Catholic Times columnist Joanna Bogle. "Yes, I write passionate things sometimes," she says, "and I criticise our bishops who scarcely can be counted as men of vigour and vision in these turbulent times, but blogs aren't necessarily the real world. I do think there is a crunch coming between the grassroots movement of young Catholics in groups like Youth 2000 who are interested in liturgy, in prayer, and above all in Jesus Christ, and the bishops who won't be able to control these movements as they challenge and renew Catholicism here."

Her criticism of the bishops reflects a minority view within the British church that would like to see them be more assertive and disciplinarian. Yet another legacy of the history of the faith here and its accommodation to the prevailing norms of the wider society has been a reluctance on the part of the hierarchy (save, perhaps, in Scotland, where they are more outspoken) to hammer home from the pulpit contentious Catholic teachings that deem homosexuality, abortion and the use of condoms sinful.

In this, the bishops are simply being realistic. Survey after survey of Catholic opinion has, for example, reported that very few follow papal teaching against contraception – hence the near extinction of the once traditional Catholic family of eight children and upwards.

Yet that pragmatism, coupled with an innate reluctance to be drawn into public confrontation, today comes at a cost when the church is being attacked from without by militant secularists. Pope Benedict may indeed want to stiffen the collective Catholic resolve.

Bishop Conry professes himself puzzled by the secularists' claims. "No one ever defines secularism," he complains. "If they mean an absence of interest in spirituality, for instance, then I would say that there is plenty of evidence of exactly the opposite." But he concedes there may be a case for him and his colleagues to engage in "a little more searching and even brutal debate". It will be music to the pope's ears.

Peter Stanford is a former editor of the Catholic Herald. His latest book, The Extra Mile: A 21st Century Pilgrimage, is published by Continuum