Many COVID restrictions are against Charter rights.
They're not against Charter Rights because section 1 sets out what is considered valid:
1. Canadian Charter of Rights and Freedoms guarantees the rights and freedoms set out in it subject only to such
reasonable limits prescribed by law as can be
demonstrably justified in a free and democratic society.
Protecting the public from a grave risk to their life and health in this case is demonstrably justified and therefore reasonable.
Canadian Rights are not nor have they ever been
absolute rights. For that reason, the rules are not against the Charter at all. The correspond with the very first section.