From the decision:

“S regularly attended the public meetings of the municipal council of the City of Saguenay. At the start of each meeting, the mayor would recite a prayer after making the sign of the cross while saying [translation] “in the name of the Father, the Son and the Holy Spirit”. The prayer also ended with the sign of the cross and the same words. Other councillors and City officials would cross themselves at the beginning and end of the prayer as well. In one of the council chambers, there was a Sacred Heart statue fitted with a red electric votive light. In another, there was a crucifix hanging on the wall. S, who considers himself an atheist, felt uncomfortable with this display, which he considered religious, and asked the mayor to stop the practice. When the mayor refused, S complained to the Commission des droits de la personne et des droits de la jeunesse. He argued that his freedom of conscience and religion was being infringed, contrary to ss. 3 and 10 of the Quebec Charter, and asked that the recitation of the prayer cease and that all religious symbols be removed from council chambers.

The Commission limited its investigation to the question whether the prayer was discriminatory. It considered the evidence to be sufficient to submit the dispute to the Human Rights Tribunal, but it did not do so itself, because the Tribunal had recently decided a similar case and because it considered S to be in a position to defend his individual rights by himself. S then pursued his remedy, with the support of the Mouvement laïque québécois (“MLQ”), by means of an application to the Tribunal. The City then adopted a by-law whose purpose was to regulate the recitation of the prayer, and that also changed the wording of the prayer and provided for a two‑minute delay between the end of the prayer and the official opening of council meetings. The mayor and the councillors continued to act in the same way as described above, however, and S and the MLQ amended their motion to ask the Tribunal to declare the by‑law to be inoperative and of no force or effect in relation to S.

The Tribunal granted the application, finding that the prayer was, when considered in light of its context, religious in nature and that the City and its mayor, by having it recited, were showing a preference for one religion to the detriment of others, which constituted a breach of the state’s duty of neutrality. The Tribunal also concluded that the prayer and the exhibiting of religious symbols resulted in an interference with S’s freedom of conscience and religion that was more than trivial or insubstantial, and that the interference was discriminatory. It declared the by-law inoperative and invalid, ordered the City and the mayor to cease the recitation of the prayer and to remove all religious symbols from the rooms where the council’s meetings were held, and awarded $30,000 in compensatory and punitive damages to S. It refused to award the reimbursement of extrajudicial fees, however, because, in its view, the City and the mayor were not guilty of an improper use of procedure.

The Court of Appeal allowed the appeal. In its opinion, the question of the religious neutrality of the state was a matter of importance to the legal system that required the application of the standard of review of correctness. It held that the prayer at issue expressed universal values and could not be identified with any particular religion, and that the religious symbols were works of art that were devoid of religious connotation and did not affect the state’s neutrality. According to the Court of Appeal, S had not been discriminated against on the ground of freedom of conscience and religion. The interference, if any, was trivial or insubstantial."

The S.C.C. (unanimously, with 1 judge writing reasons concurring in part) allowed the appeal.

Justice Gascon wrote as follows (at paras. 1, 3-4, 76, 78, 88, 122, 134, 145-149):

"The state is required to act in a manner that is respectful of every person’s freedom of conscience and religion. This is a fundamental right that is protected by the Quebec Charter of human rights and freedoms, CQLR, c. C‑12 (“Quebec Charter”), and the Canadian Charter of Rights and Freedoms (“Canadian Charter ”). Its corollary is that the state must remain neutral in matters involving this freedom. The interplay between freedom of conscience and religion, on the one hand, and this duty of neutrality, on the other, is sometimes a delicate one.

…

The Quebec Human Rights Tribunal (“Tribunal”) concluded that the recitation of the prayer was in breach of the state’s duty of neutrality and that it interfered in a discriminatory manner with Mr. Simoneau’s freedom of conscience and religion. The Court of Appeal reversed that decision on the basis that the prayer was non‑denominational and fundamentally inclusive. According to the Court of Appeal, such a prayer could not interfere with Mr. Simoneau’s rights.

…Through the recitation of the prayer at issue during the municipal council’s public meetings, the respondents are consciously adhering to certain religious beliefs to the exclusion of all others. In so doing, they are breaching the state’s duty of neutrality. The resulting discriminatory interference with Mr. Simoneau’s freedom is supported by the evidence the Tribunal accepted.

…

When all is said and done, the state’s duty to protect every person’s freedom of conscience and religion means that it may not use its powers in such a way as to promote the participation of certain believers or non‑believers in public life to the detriment of others. It is prohibited from adhering to one religion to the exclusion of all others. Section 3 of the Quebec Charter imposes a duty on the state to remain neutral in this regard. Today, the state’s duty of neutrality has become a necessary consequence of enshrining the freedom of conscience and religion in the Canadian Charter and the Quebec Charter.

…

With respect, what is in issue here is not complete secularity, but true neutrality on the state’s part and the discrimination that results from a violation of that neutrality. In this regard, contrary to what the Court of Appeal suggested, I do not think that the state’s duty to remain neutral on questions relating to religion can be reconciled with a benevolence that would allow it to adhere to a religious belief. State neutrality means — and the Court of Appeal in fact agreed with this (at paras. 76 and 78) — that the state must neither encourage nor discourage any form of religious conviction whatsoever. If the state adheres to a form of religious expression under the guise of cultural or historical reality or heritage, it breaches its duty of neutrality. If that religious expression also creates a distinction, exclusion or preference that has the effect of nullifying or impairing the right to full and equal recognition and exercise of freedom of conscience and religion, there is discrimination.

…it is essential to review the circumstances carefully. If they reveal an intention to profess, adopt or favour one belief to the exclusion of all others, and if the practice at issue interferes with the freedom of conscience and religion of one or more individuals, it must be concluded that the state has breached its duty of religious neutrality. This is true regardless of whether the practice has a traditional character.

…

At the risk of repeating myself, the attempt at accommodation provided for by the City in the By‑law, namely giving those who preferred not to attend the recitation of the prayer the time they needed to re‑enter the council chamber, far from tempering the discrimination, exacerbated it.

…

In short, there is a distinction between unbelief and true neutrality. True neutrality presupposes abstention, but it does not amount to a stand favouring one view over another. No such inference can be drawn from the state’s silence. In this regard, I will say that the benevolent neutrality to which the Court of Appeal referred is not really compatible with the concept of true neutrality. As understood by that court, neutrality would in the instant case require tolerance for the state’s profession of a clearly identified religious belief on the basis of tolerance for its history and culture. I do not believe that is the sense of true state neutrality with respect to freedom of conscience and religion.

…

The preamble to the Canadian Charter reads as follows:
Whereas Canada is founded upon principles that recognize the supremacy of God and the rule of law:

In my opinion, the respondents’ argument in this regard truncates the analysis on the issue of freedom of conscience and religion. Contrary to what their argument suggests, that analysis is not limited to a single reference to God in the prayer. On its own, that reference is not determinative. Rather, the analysis concerns the state’s observance of a religious practice. The moral source of that practice, whether divine or otherwise, is but one of the contextual factors that make it possible to identify the practice’s purpose and its effect. It is that purpose and that effect that are determinative of the existence of discriminatory interference with freedom of conscience and religion and of a breach of the state’s duty of neutrality.

The reference to the supremacy of God in the preamble to the Canadian Charter cannot lead to an interpretation of freedom of conscience and religion that authorizes the state to consciously profess a theistic faith. The preamble, including its reference to God, articulates the “political theory” on which the Charter’s protections are based (see Reference re Remuneration of Judges of the Provincial Court of Prince Edward Island, [1997] 3 S.C.R. 3, at para. 95, in which the Court was discussing the preamble to the Constitution Act, 1867 ). It must nevertheless be borne in mind that the express provisions of the Canadian Charter , such as those regarding freedom of conscience and religion, must be given a generous and expansive interpretation. This approach is necessary to ensure that those to whom the Canadian Charter applies enjoy the full benefit of the rights and freedoms and, thereby, that the purpose of that charter is attained (Doucet‑Boudreau v. Nova Scotia (Minister of Education), 2003 SCC 62, [2003] 3 S.C.R. 3, at para. 23; Big M, at p. 344; Hunter v. Southam Inc., [1984] 2 S.C.R. 145, at p. 156). The same is equally true of the Quebec Charter.

Thus, the reference to God in the preamble cannot be relied on to reduce the scope of a guarantee that is expressly provided for in the charters. Professor L. Sossin explains this as follows in “The ‘Supremacy of God’, Human Dignity and the Charter of Rights and Freedoms” (2003), 52 U.N.B.L.J. 227, at p. 229:
The reference to the supremacy of God in the Charter should not be construed so as to suggest one religion is favoured over another in Canada, nor that monotheism is more desirable than polytheism, nor that the God‑fearing are entitled to greater rights and privileges than atheists or agnostics. Any of these interpretations would be at odds with the purpose and orientation of theCharter, as well as with the specific provisions regarding freedom of religion and conscience under s. 2 . [Emphasis added.

This leads me to conclude that the reference to the supremacy of God does not limit the scope of freedom of conscience and religion and does not have the effect of granting a privileged status to theistic religious practices. Contrary to what the respondents suggest, I do not believe that the preamble can be used to interpret this freedom in this way."

Note: This summary is drawn from a Canadian Press article and the body is drawn from Eugene Meehan’s SupremeAdvocacy Weekly Updates for the Law Community.