[...] there are two places where ca_certificate can be in the config. When running from scratch, and generating this config, the content of my pem-file seemed to be put within the profiles part of the config. That gave me issues [...].
After some trial and error I ended up with:
humioctl profiles set-default default --ca-certificate-file /Users/user/.humio/cert.pem
Result was that the content of my pem-file was put in the config again, but this time outside of the profile part. This seems to work.