Thinking It Through Brings Clarity
So what is an atheist who believes in a single secular public school system supposed to think about noon hour Muslim prayers in public schools.
The answer should be simple but first let us look at the context.
In the province of Ontario there are two publicly funded school systems, one for a specific religion and one for everybody else (all other religions and non-religious persons). If one did not have an understanding of the province's constitutional history, one might assume the religion with the separate school system was the largest religious group in the province, but actually it is the second largest group that gets special treatment.
This religion has it's own school system where they are allowed to indoctrinate students in their religion and adopt policies that provide "when there is an apparent conflict between denominational rights and other rights, the board will favour the protection of the denominational rights".
While the Roman Catholic Church, and it's separate school boards, may be exempt from the Canadian Charter of Rights and Freedoms (Constitution Act, Section 29), I cannot ignore it.
Thus, as long as one religion is allowed to have it's own publicly funded school boards in which to indoctrinate students, the minimum reasonable accommodation that should be made for other religions, in the name of equality, is to allow them to use school facilities for prayer services for the convenience of students, as long as no one is compelled to attend such services.
The real solution, of course, is a constitutional amendment to remove discriminatory rights given to one religion and provide for one secular public school system in Ontario, as has been done in other provinces, including Quebec.