He was detained in the Bloomfield Avenue area, close to the Connswater shopping centre, on Saturday afternoon.
He has been charged with two counts of assaulting police, disorderly behaviour, obstructing traffic in a public place and three counts of resisting police.
He is due to appear at Belfast Magistrates' Court on Monday. As is normal procedure all charges will be reviewed by the PPS.
An ambulance was called to the scene of the arrest.
Officers confirmed medical assistance was sought but no medical assistance was required.
PUP leader Billy Hutchinson has criticised the PSNI over the man's arrest, describing it as "totally unacceptable".
He has called for a meeting with Chief Constable Matt Baggott.
"I've seen the footage of the incident and was shocked by it," said Mr Hutchinson.
"When arresting someone police officers have to take action that is both reasonable and proportionate. Based on what I've seen, I would say that this appears to be neither.
"I'm asking to meet with the Chief Constable to discuss this incident and the police response in general. There has been a lot of talk recently about the police being more affirmative in responding to the flag protests, but this appears to be totally unacceptable."
However police have defended their handling of the arrest.
A PSNI statement said: "Police were managing a protest in the Newtownards Road/Bloomfield Avenue area of Belfast when they arrested a 42-year-old male for resisting arrest, assault on police, obstruction of a public road and disorderly behaviour.
"The Police response to this arrest was appropriate and proportionate to the circumstances."
It is understood police also came under attack from missiles from the crowd.
A PSNI spokeswoman said the matter has been referred to the Police Ombudsman of Northern Ireland (PONI) for investigation.
Earlier a flag protest at Belfast City Hall passed off without incident.
Meanwhile police in Newtownabbey have made one arrest when dealing with "minor disorder" in the Cloghfern Corner area on Saturday night.
Police said calm has been restored and all roads have re-opened.