I would consider this not really a typical WP question – maybe you should ask over at http://unix.stackexchange.com – but maybe this could already help anyways:
If you have access to the server config and you know the IP address of FB Instant Articles and Apple News you could for example block everybody from accessing your feed – but allow FB Instant Articles and Apple News to access it – with something similar to this:
<Location /feed>
Order Deny,Allow
Deny from all
Allow from 1.1.1.1
</Location>
…as answered on unix.stackexchange.com (this will however NOT work in .htaccess)