Irish News editor Noel Doran said they had "got it wrong" over flag protests.
Loyalist protests followed Belfast City Council's vote last December to limit the flying of the union flag from city hall.
Some of the demonstrations resulted in violence.
On Saturday, Mr Doran told the conference in Lurgan, County Armagh, what had been opposed had been a "democratic decision" of Belfast City Council.
Mr Doran told about 140 delegates that nationalists and unionists often viewed each other with "mutual incomprehension" even though they had a lot in common.
He said loyalists could learn from organisations like the Gaelic Athletic Association, when it came to issues like community pride and reaching out.
Progressive Unionist Party councillor John Kyle said loyalists had to do "more than" protest; he said they also had to come up with ways out of problems that arose.
He said the party would not give "cover or excuse" to criminality.
Party leader Billy Hutchinson was asked about a recent shooting attack in east Belfast in which a 24-year-old woman suffered injuries to her lower abdomen, hips and knees.
Police have said they are treating the attack at Lord Street Mews as attempted murder.
There has been speculation that the UVF were behind the shooting.
Mr Hutchinson said he condemned it.
"I'm not the leader of the UVF, I'm the leader of the PUP, but I will answer it, it was despicable," he said.
"I said that at the time, irrespective of who was responsible, there's no place for those people in society and they should be removed."
During the conference, delegates also passed a motion supporting equal marriage in Northern Ireland.
The motion was: "This party joins with remainder of UK in enshrining into law equality for all in marriage.'
Meanwhile, party chairman Brian Lacey said he did not recognise the party as it was sometimes portrayed by the media, adding that if it were like that he would not be a member.
He said he was proud to be a party member adding that membership had tripled in the past year.

Rifleman William Aldridge of Bromyard, Herefordshire, was 18 when he died trying to save comrades in 2009.
A plaque commemorating his sacrifice was unveiled in the town's St Peter's Church.
It followed a campaign for a permanent memorial by William's mother, Lucy Aldridge.
She said she was "absolutely delighted" that her son, killed by a bomb in Helmand province, had received "the recognition he deserved in his home town".
The service on Saturday afternoon coincided with William's regiment, The Rifles, being given the freedom of Bromyard.
A ceremony took place in Market Square, with a parade of service personnel through the town.
Among them were representatives of William's 2nd Battalion, the Hereford company of 6th Battalion The Rifles, the Bromyard platoon of Hereford and Worcester Army Cadet Force, Herefordshire Light Infantry, and the King's Shropshire Light Infantry.

The patents include one that relates to the front face of the iPhone and one for touch-screen technology.
It is another win for Apple, after it was awarded $1.05bn (£652m) in damages by a jury in a separate case in August.
The ITC can block the import of products into the US.
The judge's ruling will go in front of a full commission, which is scheduled to conclude its investigation in February.
Judge Thomas Pender agreed that Samsung violated four of Apple's patents, but was not in violation of two others listed by Apple in the complaint.
Three of the patents are related to software features, while one covers Apple's hardware.
However, the Samsung products in this case do not include its latest devices, limiting the impact of a potential import ban into the US.
Samsung has repeatedly argued that any sales ban would limit choice and raise prices for consumers in the US.
Apple and Samsung have bought legal cases against each other in more than 10 countries, each accusing the other of violating patents, as the two battle for market share in the hugely lucrative mobile industry.
A representative of the nationalist community in Northern Ireland has addressed the Progressive Unionist Party's annual conference for the first time.
[NEXT_CONCEPT]
The youngest British soldier to be killed in Afghanistan has been honoured in his home town - seven years after he died.
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A US International Trade Commission judge, in a preliminary ruling, said Samsung infringed four of Apple's intellectual property patents.