This did violate the Canadian charter of human rights.

Do you mean the Charter of Rights and Freedoms?

In the case that this article is referring to Justices Frederica Schutz, Michelle Crighton and Dawn Pentelechuk of the Alberta Court of Appeals wrote that “Ms. Lewis’ COVID-19 vaccination status is not who she is,” the court wrote. “It is not an immutable personal characteristic … her choice not to get vaccinated against COVID-19 is just that — a choice.”

What that means is that it isn't a Charter issue because it was her choice not to be vaccinated which resulted in her being lawfully denied a transplant. It is the same for people who were not vaccinated and could not fly, it was their choice and therefore not a Charter issue.

There are excellent references available on the Justice Canada website that explain exactly what the Charter does and does not mean. Avoid Facebook because that is likely how you ended up confused in the first place and avoid the Justice Center for Constitutional Freedom website because they lose 99% of their cases because they are just a right wing extremist troll farm.