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.
A representative of the nationalist community in Northern Ireland has addressed the Progressive Unionist Party's annual conference for the first time.