This case was about taking citizenship away from Canadian citizens.  Period.

As to your other point about who the Charter protects............

1.  The Charter of Rights protects people by restricting the actions of the Canadian government.  

2.  The people protected against the actions of the Canadian government are, as set out in various sections of the Charter: "citizens,"  "every person who has the status of a permanent resident of Canada," and "everyone."

3.  That wording was approved by the elected Parliament of Canada and 9 of the 10 elected provincial legislatures in Canada.