By today's standards such a definition of religious freedom, omitting atheists, is inadequate, but at the time it was a huge step forward.
By my standards, freedom of religion doesn't mean the right to pracitce the religion of your choice (or no religion). It means freedom from domination by any religion.
In Canada, the dominant religion is Roman Catholicism. Those of us who are not Catholics don't want our government dominated by Catholics or Catholic ideas. (Of course, many Catholics don't want that either.) For that reason, fundamentalists in Canada seem quite happy with separation of church and state.