But the east Belfast MP, who has been living under the shadow of a death threat issued amid the related tensions, doesn't feel that a newly created Unionist Forum is the answer to the problem.
"We need to address difficult issues together, not separately," Ms Long said, in the wake of a night of rioting in parts of her constituency.
She believes that the flag situation has become "totemic of wider discontent", but that democracy cannot be compromised to appease a minority.
"We can't move on and leave some people behind," Ms Long told UTV's Marc Mallett on Friday.
"But we equally can't allow some people to completely impede progress."
In a new statement, First Minister Peter Robinson strongly condemned the street violence.
The violence and destruction visited on the PSNI is a disgrace, criminally wrong and cannot be justified.
Peter Robinson, DUP
Mr Robinson said those behind the unrest were playing into the hands of dissident republicans.
"Those responsible are doing a grave disservice to the cause they claim to espouse and are playing into the hands of those dissident groups who would seek to exploit every opportunity to further their terror aims," he said.
Meanwhile Ms Long said she is hoping for inclusive dialogue and feels that is the best way to find a resolution.
"What we need is a shared future approach, where we can sit down and have rational conversation around how we develop expressions of identity that are respectful, legal, inclusive and welcoming, rather than hostile," she said.
"I think that's a conversation that really hasn't been had yet. I don't think having it purely within unionism is a solution to this problem."
The Unionist Forum, to be chaired by Mr Robinson and UUP leader Mike Nesbitt, was established after UDA leader Jackie McDonald held recent talks with the DUP and UUP.
It will not be a decision-making body but will "meet to consider matters of interest and concern to the unionist community", according to a statement.
At the start of December, a motion was to be put before Belfast City Council calling for the Union flag to no longer fly above City Hall.
The Alliance tabled an amendment which, when passed, allowed the flag to fly on a number of designated days - in line with protocol at Stormont and in other parts of the UK.
On Friday the DUP leader described the move as "ill-considered and provocative".
It's not the decision which caused the problem for traders - it's the violence, the protests and the disruption ... The council didn't make that decision.
Naomi Long, Alliance
"All right-thinking unionists will want to channel their energies into political activity and to support the cause of finding political solutions to the problems that we face," Mr Robinson said.
"The real purpose of those who claim to speak for some of the organisers of the protests is fast becoming clear," he added.
"It is a straight-forward politically motivated attempt to undermine the DUP as the voice of unionism despite our attempts to oppose the removal of the Union Flag in Belfast."
Protests have been held in the weeks since the decision was taken, causing disruption to traffic and local businesses. Peaceful demonstrations have also been hijacked on a number of occasions.
Among the worst of the violence, a petrol bomb was thrown into a police car with two officers inside and elected representatives were attacked. A total of 65 PSNI officers have been injured.
Questions have been asked about the timing of the issue being raised at Belfast City Council, given the impact in the run up to Christmas and over the festive period.
"I would argue that there's never a right time to take a difficult decision," Ms Long said, pointing to summer tourism, the World Police and Fire Games and the G8 summit which could equally have been impacted had the timing been different.
While the Alliance MP has strongly condemned the violence and says the situation is certainly dangerous, she feels the police are doing their best to keep control amid difficult conditions.
Many flags flown are not contentious, but others mark out territory. Communities, particularly in mixed areas, are entitled to some protection from having this happen against their will.
Conall McDevitt, SDLP
Meanwhile, SDLP MLA Conall McDevitt has also spoken out against the violence and the increase levels of "territorial" flag flying.
"Those who are seeking to bring violence onto our streets are defeating their own argument and the community must unite in condemnation of these acts," the South Belfast representative said.
"Added to this, over the past month there has been a significant increase in the aggressive and intimidatory flagging of mixed neighbourhoods across Belfast and elsewhere in the North.
"These actions are unjustified and undermine any cause, instead reinforcing people's perception that this is about domination rather than respect for different identities."