The media coverage surrounding this issue has made me realize that many Canadians are confused about whether the Charter guarantees the separation of church and state. It does not. Further, our constitution lacks a clear equivalent to the most famous of such constitutional protections—the American establishment clause.
The establishment clause is a phrase in the 1st Amendment of the U.S. Bill of Rights that says "Congress shall make no law respecting an establishment of religion". Canada has no equivalent constitutional protection.
Although the linked National Post article above focuses on the up-coming human rights complaint, on the Charles Adler show on the afternoon of December 18, 2012, Mr. Solo implied that Canada has constitutional protection regarding the separation of church and state.
If I had to guess, I would say that Mr. Solo, and other Canadians like him, are confused because they have watched US legal dramas on TV and assume that, like the U.S., Canada has a similar separation of church and state. We do not. Consider this plain and simple fact: the Queen remains the Head of State in Canada even though she is the Supreme Governor of the Church of England.
On the other hand, section 2 of the Charter does guarantee "freedom of religion", and the courts have interpreted this to include a right to be free from religion.
But this right to be free from religion is subtly, yet significantly, different from a separation of church and state. Freedom of religion under the Charter means that Canadians are free to practice their religions in a non-harmful fashion (e.g. the Multani case), while freedom from religion means that Canadians cannot be forced to adopt a religious practice (e.g. the Big M Drug Mart case).