Jim Dowson, 48, a former British National Party (BNP) fundraiser originally from Cumbernauld, was granted bail on strict conditions at Belfast Magistrates Court, while Jamie Bryson, 23, was refused bail.
Dowson,now residing at The Burn Road, Comber, Co Down, was charged with encouraging or assisting offenders and five counts of taking part in an unnotified public procession.
Bryson, from Rosepark in Donaghadee, Co Down, has been charged with two counts of encouraging or assisting offenders and four counts of taking part in an unnotified public procession.
The protests have been continuing since early December when Belfast City Council voted to limit the number of days the flag flew over City Hall.
A number of the earlier demonstrations descended into violence, particularly in east Belfast, with around 140 police officers being injured.
The demonstrations have become more sporadic and less incendiary in recent weeks, though tensions still surround a weekly march from east Belfast to the City Hall.
While police have said peaceful protests are legal, they have warned that mass parades to such events that have not been notified to Northern Ireland's Parades Commission are against the law.
Both Bryson, who is chairman of protest group the Ulster People's Forum, and Dowson have been charged in connection with participation in such unnotified parades.
Appearing in the dock, Dowson, dressed in a navy suit, light blue shirt and red tie, only spoke to confirm he understood the charges.
Connecting him with the charges, a female police constable said she was opposing his bail application on the grounds of likelihood of re-offending.
She said community tensions around the flag issue were still high and public disorder could escalate.
The officer said police believed Dowson would encourage others to commit offences.
She then read from an extract of a speech the defendant allegedly delivered to the media outside City Hall yesterday when she said he spoke of a "wake up call to the people of Ulster" and it being "a time to get on the streets".
But Darren Duncan, representing Dowson, insisted his client's remarks referred to getting out to vote.
He said he later addressed protesters at City Hall and urged them not to take part in a parade as they might get arrested.
The officer replied: "He does not mention the word voting, he is asking people to get on to the streets."
The constable said Dowson was later seen moving at the head of a group of 40 to 50 people in east Belfast.
But his lawyer insisted he had been trying to distance himself from the crowds.
Mr Duncan told the judge that his client had a young family and was the director of a business in Dundonald in greater Belfast.
"He wishes to be home with his family and is willing to consider any condition the courts would impose," he said.
District Judge Bernie Kelly Kelly said she would grant bail on strict terms. Those included agreement not to use any form of communication device both at home and at work, a ban on entering Belfast and on being within 1,000 metres of any parade.
She said any communication deemed to be made on Dowson's behalf would constitute a breach of bail, which she set at £1,000 with a further £1,000 of sureties. He is to appear in court again at the end of the month.
Bryson, dressed in a blue jumper and checked shirt, shook his head as Judge Kelly refused his bail application and remanded him in custody. He had spoken earlier only to confirm he understood the charges against him.
A detective constable, who said he could connect Bryson with the charges, had opposed bail on the grounds that the defendant would likely re-offend and was a flight risk.
He described Bryson as a "main player" in "organising" the unnotified processions and said he regularly encouraged people to participate both through public speeches, delivered by megaphone, and media interviews.
In regard to the risk of flight, the officer noted that Bryson had refused a police request to come forward for questioning prior to his arrest on Thursday and at the time had given a TV interview stating he would not hand himself in.
When he was eventually detained he was found in a locked room, the officer added.
Mr Duncan, also representing Bryson, asked why his client had not been charged with organising the parades if that was what the police believed he had done.
He also questioned how people were meant to get to legal protests if groups travelling there were deemed to be breaking the law. The lawyer compared the scenario to crowds walking en mass to a sporting fixture.
"If someone is going to a lawful protest how do they get there?" he said.
Mr Duncan insisted his client had never taken part in or encouraged violence. "In no way is he responsible in any shape or form for any violence," he said.
Noting Bryson's parents were in court, he said they had had a "lengthy conversation" with their son and were confident he would comply with any bail conditions.
"This is a person who has never been in prison before," the lawyer added.
"He stands here facing the prospect of going to prison for the first time."
Refusing bail, Judge Kelly said her main concern was the events leading up to his arrest where he had seemingly avoided the police through a deliberate act.
"For that reason I am not releasing him on bail," she said.
Bryson will appear again in court via videolink on March 20.
Yesterday another high profile flag protester, 52-year-old Willie Frazer from Markethill, Co Armagh, was remanded in custody after appearing in court charged with a series of offences linked to the dispute.