Police received report of the incident on Friday night and confirmed the car was not damaged.
Local Sinn Féin MLA Cathal Ó hOisín said the PSNI need to do more to protect motorists and pedestrians during flag demonstrations after he received report that a stone had been thrown.
"While I recognise the right to peaceful protest it is clear that many of these flag protests have been illegal or had violence and intimidation associated with them," Mr Ó hOisín said.
"I have been in contact with the local PSNI Commander to register my anger and disgust at how this woman travelling to her work was treated while PSNI officers looked on.
"The PSNI have a responsibility to combat illegal activity and protect citizens going about their lawful business yet there are many examples of them abdicating their responsibility during the ongoing flag protests and this is not acceptable.
"I will be expecting answers from the PSNI and guarantees that they will tackle crime no matter from where it emanates."
Police did not confirm if stones had been thrown at any vehicles during the demonstration.
It is understood protestors did not block the roads.
PSNI have previously stated that obstructing the road is an offence and that anyone who endangers someone else's safety during the pickets is also causing an offence.
"Individuals have the right to peaceful, lawful protest, in line with the Human Rights Act. Police will act appropriately to ensure that there is no unnecessary disruption caused to the public by such protest," a PSNI spokesperson said.
Loyalist flag protests have been held across the region since a Belfast City Council vote in December to reduce the number of days the Union flag flies at City Hall.
The Ulster People's Forum said last month they were changing strategy from road blocks to legal white line pickets, but added that they did not represent all those protesting.