They are denouncing the Muslim Brotherhood as terrorists and insisting the ouster of Islamist leader Mohammed Morsi was not a coup.
The protesters are chanting "down with the Brotherhood" and demanding Obama not interfere with the military's crackdown.
Twenty-four-year-old Vivian Michael says Egyptian-American groups and Coptic Christian churches organized the protests. She says if Obama can't support Egypt's transition, he at least should not condemn it.
Security officials say the protests are peaceful ,and there have been no arrests.
The Obama administration is conflicted over whether to cut off Egyptian aid. The US wants to continue aiding Egypt's military-backed government to maintain ties and regional influence. But it doesn't want to condone the bloody crackdown on Morsi's supporters.