Vatican officials acknowledged, from the start, they were not expecting cheering crowds to welcome Pope Benedict.
Instead, thousands of Turks took to the streets in Istanbul, Sunday, to protest the visit and even the Turkish government had signaled its displeasure. Prime Minister Recep Erdogan initially said his schedule would not permit a meeting with the pontiff but, in the end, a quick greeting was arranged at the airport for the Pope's arrival, as the prime minister prepared to leave for the North Atlantic Treaty Organization summit in Latvia.
This is Pope Benedict's first visit to a predominantly Muslim country since he became head of the Roman Catholic Church, last year. And, many people here say he has some fence mending to do.
In a speech two months ago, the Pope quoted a 14th Century Byzantine emperor, who characterized some of the teachings of the Prophet Muhammed as "evil and inhuman," and spoke of the spread of Islam mainly "by the sword."
That led to protests by Muslims in Turkey and other countries, who believed that the pontiff - even though he was quoting someone else - had insulted their religion. Some of the protests turned violent, including in Somalia, where Muslims angered by the Pope's remark killed a Roman Catholic nun.
Professor Dogu Ergil, a political sociologist at Ankara University, says the Pope was really expressing a deeply held view in the West: that Islam poses a threat to Christianity.
"In fact, he was voicing a concern in the Christian world that Islam grew to be (a) more resilient and more dynamic religion today and was encroaching on the world of Christianity or trying to invade both the private space and the geographical space of Christianity, " the professor said.
Many also see a concern about Islam as a root cause for Benedict's views about Turkey's place in Europe - views he expressed long before he became pope.
Political scientist Hasan Uelan, of Ankara's Bilkent University, says those views have infuriated even many secular Turks.
"We remember this pope, as Cardinal Ratzinger in Rome and he used to come up with unsolicited advice and remarks about Turkey's EU [European Union] prospects and each time he would open his mouth then what would come out would be things like cultural differences between Turkey and the European Union, civilizational differences," he said.
Uelan belongs to the Euro-skeptics in Turkey, who are not eager for Turkey to become a full-fledged EU member. Still, he says he was hurt by the Pope's comments.
After a low-key day in Ankara, the Pope travels to Ephesus, Wednesday, to say mass, before going on to Istanbul for meetings with Patriarch Bartholomew I - the spiritual head of Orthodox Christians. These meetings are the original purpose of the Pope's visit to Turkey. He is expected to concentrate on relations between the Orthodox and Roman Catholic Churches - relations that have often been strained over the centuries.
The Pope's trip comes at a time of heightened tensions between the West and Islam. Still, a Turkish government spokesman expressed hope that this could all be left behind and that the Pope's visit would mark a turning point in relations between the two faiths. But, many wonder how likely that will be, amid loud and angry protests. Many Turks insist the Pope is a guest and will be treated with customary eastern hospitality. But, the government is taking no chances and thousands of extra police have been deployed. According to officials here, security measures taken for the Pope are even tighter than those taken for President Bush, during a 2004 NATO summit.