It means that if you protect a page from being accessed by those who didn't pay, that'll keep search engines out too, and if you want search engines to crawl certain pages, you shouldn't protect those.
s2Member, or any other content protection plugin, would not be of much use if it showed all the protected content to the search engine, since then anyone would have access to it via the search engine's cache without paying you for it.
Basically, for SEO purposes, but also for trust building with visitors, you will need to have some public content (open to all) in addition to the protected content (paid, restricted).
I hope that makes it clear.