Critics say the Roman Catholic Church is hostile towards homosexuality, citing its stance against gay marriage and adoption by homosexual couples.
It has also come under fire for its opposition to abortion, IVF, stem cell research and the use of condoms.
Reformist Catholics are using the Pope's visit as an opportunity to call on Benedict XVI to open up the debate on priestly celibacy and the ordination of women.
In recent weeks, there been some vociferous attacks on the Pope, with some calling for his arrest over his handling of the clerical sex abuse crisis that has scandalised the Church.
Supporters of the Church, though, say the most ferocious attacks come from militant secularists and radical humanists who are disturbed by faith and want to deny religion any voice in the public square, thereby undermining their own claim to pluralism.
The nature of the Pope's trip has also proved controversial because British taxpayers have to underwrite the state's £10m share of the costs.
Here is a rundown of some of the groups who will be speaking out during the Pope's visit:
Scottish protests
Some protests are planned in Scotland, although Tim Maguire, spokesman for the Humanist Society of Scotland, said: "Scotland has a nasty and long history of sectarian violence so we are not taking to the streets to protest."
The largest Protestant grouping, the Grand Orange Order Lodge of Scotland, intends to hold a protest along the route the Popemobile will take through Edinburgh on Thursday.
It said the action would be on a smaller scale than demonstrations against the Papal visit in 1982 because, as a loyalist organisation, it did not want to offend the Queen, who will welcome the Pope at Holyrood House in Edinburgh.
Ian Wilson, head of the Grand Orange Lodge of Scotland, said the protest was not directly aimed at the Pope's visit.
"It's more to highlight the fact that this year marks the 450th anniversary of Scotland's break from Rome," he said.
Meanwhile, a 60-strong delegation from the Free Presbyterian Church will hold a protest, led by Ian Paisley, founder of the church, outside the Edinburgh building where the Church of Scotland was formed.
"I have been visited by many Roman Catholic people who are gravely pained by the actions of Rome in regard to the attacks on young children," he said.
Protest the Pope
Protest the Pope, an umbrella group bringing together a dozen humanist, atheist, secular and gay rights groups, opposes the idea of Benedict XVI being welcomed to the UK as a head of state, with the UK taxpayer paying for much of the visit.
Thousands of its supporters are poised to march through London from Hyde Park to Downing Street on Saturday in a rally that Terry Sanderson, president of the National Secular Society, described as "parallel, not confrontational".
Leading the protest will be human rights campaigner Peter Tatchell, who has called on the Vatican to release to police any documents it has about the abuse of children by priests.
Mr Tatchell, who attempted a citizen's arrest on Zimbabwean President Robert Mugabe during a UK visit in 1999, said he had no plans to try to arrest the Pope, although he opposed the Church's refusal to ordain women as priests.
"Women are deemed unfit to preach the Gospel," he said. "This is an insult to the whole female sex… this is pure patriarchy, sexism and misogyny."
A second protest is planned during the Pope's visit to St Mary's University College in Twickenham on 17 September with some demonstrators favouring blocking the main road to the event.
Austen Ivereigh, co-ordinator of Catholic Voices - a group set up to put the Church's view during the visit- said Protest the Pope was a loosely-aligned group with an intellectual position that had no popular support.
"What drives the secularists is a fear of faith in the public sphere, but I don't think any of them represent serious public opinion," he told the BBC.
"Most people are open to religion, even if they are not religious themselves."
Catholic Voices for Reform
Set up as a counterpoint to Catholic Voices, Catholic Voices for Reform describes itself as the Church's "loyal opposition".
It wants an open debate on issues such as women's ordination, homosexuality and clerical celibacy.
Pat Brown, spokesperson for Catholic Women's Ordination (CWO), said: "We are looking for the Church to be more collaborative and to talk and listen to people more.
"It seems to us that the church is moving backwards, not forwards."
Clerical sex abuse victims
Since 2001, the Vatican has considered sex abuse allegations concerning some 3,000 priests and dating back half a century.
The issue has scandalised the Church and victims' support groups hope to use the Pope's visit to further highlight the issue.
Victims accept the Catholic Church in England and Wales has gone further than many of its counterparts overseas in tackling the abuse issue.
The Pope himself has been accused of being part of a culture of secrecy, and of not taking strong enough steps against abusive priests when he had that responsibility as a cardinal in Rome.
His supporters vigorously deny this, saying he has been the most pro-active pope yet in confronting abuse.
In March, he wrote a letter apologising to Irish abuse victims.
He has promised to take "action", saying the Church must acknowledge its "sin within", and made clear that cases of abuse must be reported to the police.
Officials have said the Pope would meet up to 10 abuse victims privately during his UK visit.
But victims' support group Macsas (Minister and Clergy Sexual Abuse Survivors) wants to air its grievances in public.
Anne Lawrence, Macsas chairwoman, said the Church needed to establish an inquiry and work to redress survivors' grievances.
The group has compiled messages by abuse survivors that it had hoped to present to the Pope, although this request has been turned down by the Church.
SIC: BBC/UK