You are correct that flights are federally regulated but I don’t think they’ve actually restricted flights to/from Mexico. See “consolidation of inbound flights to four major hubs only”:
Aviation measures in response to COVID-19 - Transport Canada
Now, whether Canadians have to quarantine for 14 days on return is another issue, as well as whether the airlines are actually operating any flights. Of course, whether people will choose to fly is yet another issue. And of course, I think the Feds have also recommended against all non-essential international travel (but it is but a recommendation).,QUOTE]