'New way forward'
In his inauguration address on January 20, Barack Obama, the US president, vowed to seek a "new way forward" with Muslim majority countries, "based on mutual interest and respect".
|Clinton's trip to Indonesia is aimed at 'reaching out' to the Muslim world [AFP]
Clinton acknowledged on Tuesday that the war in Iraq was a key stumbling block to better US-Muslim ties.
She also said that one of the central security challenges faced by the US government is "how to better communicate in a way that gets through the rhetoric and through the demagogy and is heard by people who can make judgements about what we stand for and who we truly are".
Clinton's remarks came in response to a question about "prejudice" in the US against Muslims, a term she rejected, pointing to the history of Christians.
"I am a Christian," she said.
"Through the centuries we have had many people who have done terrible things in the name of Christianity. They have perverted the religion."
Security had been stepped up in Jakarta in advance of Clinton's arrival.
Thousands of policemen were deployed across the Indonesian capital as officials prepared for possible attacks from extremist groups or unrest linked to anti-US demonstrations.
Indonesia has had a love-hate relationship with the US since the 1960s, marked by US support for Suharto, who was viewed by many as a military dictator and was ousted as president in 1998.
Many Indonesians also oppose the "war on terror" launched by the previous US administration of George Bush.
Another subject likely to addressed during Clinton's visit to Indonesia is building on US economic ties with the region.
But Karim Raslan, a political analyst and commentator, told Al Jazeera there was limited scope for economic cooperation between Indonesia and the US in the wake of the global slowdown.
"The most important thing would be for a country like Indonesia to be raised to become a close economic ally of the US… and that is something the US should do for Indonesia," he said.
He said that Clinton, as a representative of the world's largest debtor nation, was coming to Asia "on bended knee", a supplicant visiting her country's largest creditors.
Analysts say Obama, who spent several years of his youth living in Jakarta, could be trying to capitalise on his emotional ties to Indonesia as he seeks to improve relations with the Muslim world.
The US faces daunting political challenges ranging from the Palestinian territories to Iran, Iraq, Afghanistan and Pakistan.