Anita McNaught, Al Jazeera's correspondent in Ankara, said the protests had been "small and quite specific".
"The protesters suspicions are that Obama has come here with a secret agenda, to pressurise the Turkish government to put combat troops into Afghanistan in an effort to help control the situation there," she said.
"But that is something the Turkish government has consistenly said it won't do."
Despite the opposition, Obama hopes his visit will strengthen ties strained by the Iraq war. He also aims to push for a bigger agenda with Turkey, a Nato member which borders Iran and Iraq as well as Europe and Syria.
While Turkey has been long regarded as a close US ally in the Muslim world, some analysts believe there has been a cooling of ties during the former US administration of George Bush.
Washington and Ankara had been sharply at odds in recent years over such issues as how to deal with Iran's nuclear programme, the rise to power of Hamas in the Palestinian territory of Gaza, and political developments in Sudan.