Hundreds of supporters turned up to hail his UN visit with chants of "Rouhani we thank you" and "Iran calls for moderation", but a smaller number of hardliners shouted "Death to America" and threw eggs at his official car leaving the airport, Iranian media reported.
The semi-official Mehr news agency said one protester threw his shoes at the vehicle, a gesture of deep insult in the Islamic faith.
While an anticipated handshake between Rouhani and Obama at the United Nations headquarters failed to materialise, they held a 15-minute call on Friday at the end of the moderate new Iranian president's trip for the UN General Assembly.
It was the first direct contact between Iranian and US presidents for 34 years.
US officials said the phone call - which focused on how to resolve the standoff over Iran's disputed nuclear programme - was requested by the Iranian side but in comments to journalists after his return, Rouhani indicated it was an US initiative.
During his visit to the UN forum in New York, Rouhani had signalled a shift in tone on Iran's controversial nuclear programme, asserting that Iran does not seek a nuclear bomb, despite long suspicions by Western powers.
Rouhani was elected by a landslide last June, buoyed by many voters keen for steps towards moderation and reform after eight years of intensifying repression at home and isolation abroad under confrontational predecessor, Mahmoud Ahmadinejad.
The contacts Rouhani and his foreign minister had with US officials during the UN General Assembly were unlikely to have happened without the approval of Iran's ultimate authority, Supreme Leader Ayatollah Ali Khamenei.
However, the polarised reactions on Rouhani's return have hinted at the challenge he faces in winning over anti-Western hardliners, especially in the powerful clerical and security establishments, to his conciliatory approach.