"I think it's a couple of fundamental values that transcend any one faith ... respect and fairness," Premier Dalton McGuinty told reporters.
"We do everything we can in the confines of our homes to love and respect and accept our children. We just want to make sure the same kind of atmosphere prevails in publicly funded school systems."
Thomas Cardinal Collins, Archbishop of Toronto, accused the Liberal government of infringing on religious freedom by amending its anti-bullying bill to say Catholic schools must allow student clubs to use the word "gay" in their names.
McGuinty dismissed the Cardinal's argument.
"We’re not mandating the terminology gay-straight alliance," he said, "but we think it’s very important students should so choose to be able to use that language."
McGuinty, who is Roman Catholic and whose wife Terri is a teacher in the separate school system, said his job is to look out for everyone.
"Cardinal Collins has his responsibilities ... but I have a different set of responsibilities," he said.
"I’m accountable to people of faith, and people of no faith. I’m accountable to all parents, and I think the fact that I know we have something in common as parents — we want to make sure our kids are accepted and respected for who they are."
Collins said he has frequently heard the argument that Catholic schools should not accept public money if they don't want to have the government tell them what to teach.
"I’m a taxpayer too of course," Collins told Toronto radio station NewsTalk 1010 Tuesday.
"We all are serving the common good, so this idea you can kind of override the religious values that serve the common good just simply on the point of public funding I think is just not a good argument."
The Roman Catholic system gets about one-third of Ontario's $24-billion education budget, but only 23 per cent of electors direct their education taxes to separate schools.
The Progressive Conservatives said the government has more important issues to deal with than the naming of student clubs, and suggested the Liberals targeted the Catholic Church to trigger a bigger debate on ending the separate school system.
"That’s not part of our plan," said Opposition Leader Tim Hudak.
"I don’t know if that’s what’s underlying the Liberal move to pick a fight on this issue with the Catholic system."
The Green Party of Ontario, which has no elected members in the legislature, is the only political party calling for an end to public funding of Catholic schools.
The New Democrats said people are not interested in re-opening that debate.
"I don’t think it’s time for us to get into a long, protracted, divisive argument about funding of the separate school system," said NDP Leader Andrea Horwath.
"I think what people want us to do is remember what this discussion is all about in the first place, and that’s about young people who are gay, lesbian, queer or transgendered who want to have a support system in their schools."
Education Minister Laurel Broten said the government was "absolutely not" looking to merge the two public school systems.
Broten said the Liberals were committed to observing Constitutional protections for Catholic and French schools as they look to merge boards in some areas in hopes of saving $10 million.
There are some smaller communities in Ontario that want to merge their public and Catholic school boards but the government won't even allow those discussions to take place.
"There are school boards that have advanced a desire to have a local conversation with respect to a merger and I indicated to them that that is not a conversation that we are willing to embark upon (because) it does not respect the Constitutional rights of Catholic education," said Broten.
"It does not mean though that there isn’t important collaboration that can happen in communities across the province."
As an example of that collaboration, Broten pointed to the newly built St. Basil and Walter Gretzky schools in Brantford, where Catholic and public students share a gym, library and computer technology area.
The cardinal said Catholic schools should be allowed to use their own ways to deal with homophobia and should not have to allow the use of the term gay-straight alliance to name student clubs.