Speaking in the House of Commons on Tuesday, Ms Villiers condemned the disorder in the region, reiterating: "There can be absolutely no excuse or justification for this kind of thuggish and lawless behaviour".
She said those engaged in the violence "are not defending the Union flag".
"They are dishonouring and shaming the flag of our country," she said.
She also added the disturbances were causing "untold damage" to hard-pressed traders in the run up to Christmas.
She welcomed a Stormont motion condemning the violence which was supported by all members on Monday.
There is nothing remotely British about what they are doing. They discredit the cause that they claim to support.
Secretary of State Theresa Villiers
East Belfast Alliance MP Naomi Long was at Westminster after Monday night's attack on a police car guarding her constituency office in the city.
The incident, which was the latest in a series against the party and police, has been described by the PSNI as an "attempt to kill a police officer".
"I know that the whole House will join with in expressing our complete solidarity with the Hon Lady and her colleagues in the Alliance Party and all of the people who have been threatened and intimidated over the last week," Ms Villiers added.
"The right of elected representatives to go about their daily business without the threat or fear of intimidation is one of the hallmarks of our democracy.
"And the actions of those who carry out such threats are nothing less than an attack on democracy."
Ms Long said she condemned the "wanton and gratuitous attempt to murder police officers who were guarding my constituency office, and for whom I have the utmost admiration and respect".
She asked whether the violence was being treated as a matter of national security and when Prime Minister David Cameron would meet with Justice Minister David Ford.
Ms Villiers replied: "The successes of the last 20 years demonstrate that generous leadership and being prepared to compromise can actually lead to tremendous benefits right across the community.
"I have every confidence that the political leadership in Northern Ireland is capable of that form of generous leadership on flags as it has been on so many other issues."
Ms Villiers paid tribute to police officers for their service during the ongoing unrest.
A total of 32 officers have been injured and 38 people have been arrested since the trouble began last Monday.
If we are to have a shared future, capable of dealing with emotive and charged issues such as the flying of flags, it will require strong and courageous and above all generous leadership, willing to give a little of their own position in order to gain the greater prize for the whole community.
Naomi Long, East Belfast Alliance MP
On Tuesday, Ulster Unionist leader Mike Nesbitt said he 'reluctantly" called for an end to street flag protests in Northern Ireland.
He said his announcement was made "because of the inevitability of violence and before somebody gets killed".
"Let politicians like myself with come up with an alternative strategy which allows people to celebrate their identity confidently but not aggressively."
Ms Villiers' statement followed a call from Shadow Northern Ireland Secretary Vernon Coaker for a "clear and strong political response from Westminster".
He said: "Violence night after night would not be tolerated in London, Dublin, Cardiff or Edinburgh. It should not be tolerated in Belfast. A clear and strong political response at Westminster is needed.
"The House of Commons urgently needs to discuss what is happening in Northern Ireland, and the Secretary of State should make a statement about the steps the Government are taking."
Alliance Party leader David Ford also claimed on Monday's UTV Live Tonight programme that Mr Cameron had failed to return his telephone call.
Mr Ford said there was "intense anger, hurt, distress" over the attacks against his party.
He added: "Hurt in particular that there is very little response from the Government. I sought a call today [Monday] to the Prime Minister and I haven't had that."
"Naomi Long had a meeting with the Secretary of State which was full of apology - but nothing of substance. If the deputy Prime Minister can ring an MP whose life is threatened over the weekend - I would expect the Prime Minister to take it seriously as well."
Ms Long received a death threat last week in the wake of the passing of the party's flag amendment by a majority of Belfast City Councillors.
Mr Ford added: "I think what we need is an assurance that the government takes the threat which is currently faced democracy in Northern Ireland seriously - that it doesn't think that the only threats come from Republicans, that it's prepared to ensure that the resources are supplied to face down these protests."
The Justice Minister said this was "not about peaceful protest anymore" but about "deliberate targeting."
Meanwhile Tánaiste Eamon Gilmore told the Dáil on Tuesday he spoke with Ms Villiers and Mr Ford about the violence.
He said: "The scenes of violence and intimidation remind us of the need for steady support for the peace process.
"We condemn the outbreaks of violence on the streets of Belfast and the attacks on members of the Alliance Party and on the PSNI."