Here is my setup:
Multisite with sub-sites and mapped domains
enabled global tables for Membership plugin
Membership is protecting all content except the homepage on sub-sites. Going directly to a page on the sub-sites results in the protected content page.
Each sub-site only has a few pages, most of which should be public. Only a few pages will be member-only and I could protect the content on these using shortcodes.
Thanks for any help in advance!