Because they weren't a significant portion of the populace that needed to be placated at the time.
At the time? Well thank God there was nothing about burning witches or we'd refuse to change that too? Certainly we could change the Constitution to make things equal for all, no?
From the official complaint:
"
3.1 The author contends that the legislative grant of power to fund Roman Catholic schools authorized by section 93 of the Constitution Act of Canada 1867, and carried out under sections 122 and 128 of the Education Act (Ontario) violates Article 26 of the Covenant. The author states that these provisions create a distinction or preference which is based on religion and which has the effect of impairing the enjoyment or exercise by all persons, on an equal footing, of their religious rights and freedoms. He argues that the conferral of a benefit on a single religious group cannot be sustained. When a right to publicly financed religious education is recognized by a State party, no differentiation should be made among individuals on the basis of the nature of their particular beliefs. The author maintains that the provision of full funding exclusively to Roman Catholic schools cannot be considered reasonable. The historical rationale for the Ontario government's discriminatory funding practice, that of protection of Roman Catholic minority rights from the Protestant majority, has now disappeared, and if anything has been transferred to other minority religious communities in Ontario. A 1991 census is quoted as indicating that 44% of the population is Protestant, 36% is Catholic, and 8% have other religious affiliations. It is also unreasonable in view of the fact that other Canadian provinces and territories do not discriminate on the basis of religion in allocating education funding.
3.2 The author also claims that Ontario's school funding practices violate Article 18(1) taken in conjunction with Article 2. The author states that he experiences financial hardship in order to provide his children with a Jewish education, a hardship which is not experienced by a Roman Catholic parent seeking to provide his children with a Roman Catholic education. The author claims that such hardship significantly impairs, in a discriminatory fashion, the enjoyment of the right to manifest one's religion, including the freedom to provide a religious education for one's children, or to establish religious schools."
The second paragraph is revealing. Clearly the current system has imposed costs on Waldman that a Catholic could have avoided. So no they are not treated equally.
But I'm sure some here would now argue Waldman is anti-Catholic or that the Human rights Committee is anti-Catholic for promoting equality. So be it.