Yes and no, inasmuch as government and institutional laws and actions, which the Charter and the rest of the Constitution Act of 1982 govern, affect what citizens can and cannot do or have the freedom or not to enjoy. The Charter clearly and explicitly applies to individuals when it uses, repeatedly, the phrases “Every citizen of Canada has the right to …” and “Everyone has the right to …,” and when it includes, for instance, the right to vote, and freedom of religion, and the right to move to, take up residence in, and work in any province, and the right to be informed promptly of the reason for arrest. Clearly these are rights that extend to people, not governments, though the directive is that governments at all levels ensure those rights are guaranteed and applied equally.
This is not my understanding. The Charter of Rights and Freedoms dictates that government must not discriminate on the grounds of, among other things, physical disability. But there is no one definition of disability. See Diabetes Canada’s explanation: “There is no standard definition of ‘disability’ in Canada; each federal, provincial/territorial government program and private insurer may interpret ‘disability’ differently and set their own rules for eligibility. For most programs, eligibility is based not on which disease or disability you have, but on how the disease/disability affects your ability to work, participate in society, etc.”
Some disabilities few people or institutions would quibble with: people who are legally blind, or who must use a wheelchair, for example. Other conditions require adjudication. People with diabetes, for instance, are not ipso facto eligible for the Disability Tax Credit (although various advocacy groups are pushing for that); they have to apply, and meet specific eligibility criteria, with restrictions and definitions outlined by Canada Revenue Agency, and according to Diabetes Canada, “most people with diabetes do not quality to receive [the credit].”