"Obama has promised maintaining a mutual respect with the Muslim world but the position that the U.S. shows when it attacks Pakistan and Afghanistan means it has not changed," said Heru Binawan, head of the Jakarta branch of Hizbut Tahrir Indonesia.
The suspected U.S. missiles were fired into Pakistan last week, killing at least 14 people.
It was the first strike since Obama took office.
Some of the protesters from the Muslim group Hizbut Tahrir Indonesia also held banners saying "Obama is similar to Bush".
End item/109