Cara Henderson, 33, set up Nil by Mouth after Celtic fan Mark Scott was killed. Breaking a decade-long silence on the topic, she warned the country's sectarian problem may be worse now than in 1995, when Mark died.
She spoke out after Scotland's new anti-bigotry czar Duncan Morrow said the problem was one that involved all social classes.
His comments led Catholic Church spokesman Peter Kearney to compare the plight of the faith's followers to those of black people in America in the 1950s and 1960s.
Ms Henderson, who stepped down from the charity after moving to London in 2002, still keeps in regular touch with Nil by Mouth's work and Scottish affairs.
She said she agreed with many of Mr Kearney's remarks, adding: "Scotland was, and perhaps still is, anti-Catholic," but believes the faith did not have a monopoly on being the target of hatred and distrust.
The lawyer spoke of concern that those who disagreed with the principle of faith schools were at risk from being framed as part of the bigotry problem and "as evidence of a prevalent and pernicious form of anti-Catholicism, or at least anti-religion".
She said: "Even if the respected statisticians and social scientists conclude that Scotland is, proportionately speaking, more anti-Catholic or anti-Protestant, is there anything to be gained by framing, and I would argue, limiting the debate in these terms?
"There are many people in Scotland who are anti-Catholic, but there are also many people who are anti-Protestant, anti-English, anti-British, anti-Irish, anti-Muslim.
"We all know there are many anti-Celtic and anti-Rangers fans. The list could go on. It is true that in more than a decade since Nil by Mouth was formed the problem hasn't gone away. In some respects it may even be worse."
Mark, 16, died after his throat was slashed in an unprovoked attack in Glasgow in 1995 simply because he supported Celtic.
The Glasgow Academy pupil, the son of a leading corporate lawyer, had been watching a match at Celtic Park and been subjected to abuse from Rangers fans outside a pub when Jason Campbell attacked him.
Campbell, sentenced to serve a minimum of 14 years in prison for the killing, was released in 2011. His father and uncle were members of the Ulster Volunteer Force in Glasgow.
Ms Henderson said: "Peter Kearney has made an important contribution to the debate, provocative as his words have been. I agree with a lot, if not everything he has said on the issue of sectarianism.
"I agree that anti-Catholicism was for a long time the elephant in the room. I thought it, but I never did dare say it. It is probably not the right way to go.
"Whatever the answers, and there will be many and sometimes conflicting ones, above all else we need to keep asking questions.
"We need to keep the debate open. We can't shut it down, either by sweeping it under the carpet or by setting up conceptual dead-ends."
Meanwhile, Mr Morrow said the cessation of Old Firm hostilities after Rangers financial implosion forced the club to play in the third division had created space for his year-long examination of sectarianism as head of a Holyrood advisory group on how to tackle the problem.
He said part of his remit would involve exploring whether Old Firm hositility was "90-minute bigotry which stops the minute you leave the terraces, or something which spills out and impacts on the way people treat each other".
He added: "In some ways it also creates a window within which it's not about which club is going to win the Premier League and we can stand back a little bit. It's slightly less heightened.
"Everybody knows at times of heightened rivalry between the football teams things have happened around that."