The Charter does not say that all religions are equal, either. The Queen, despite being both our head of state and head of the Church of England, has no power to enforce Anglicanism on us. What makes different from Iran or Saudi Arabia is that we have protections for religious freedom (rather than, y'know, throwing Christians in jail or worse). Here are the relevant passages in the Charter:

2. Everyone has the following fundamental freedoms:
(a) freedom of conscience and religion;
(b) freedom of thought, belief, opinion and expression, including freedom of the press and other media of communication;
(c) freedom of peaceful assembly; and
(d) freedom of association. 

27. This Charter shall be interpreted in a manner consistent with the preservation and enhancement of the multicultural heritage of Canadians.

I'm pretty sure that Iran and Saudi Arabia don't have clauses designed to preserve and enhance their country's multicultural heritage.