Google doesn't penalize links from social media websites because the vast majority of them are rel="nofollow". And as long as they are nofollow they will not impact rankings. Therefore, there is no reason to penalize your site. The links are already worthless for ranking purposes.
In regards to Facebook specifically, there are many pages on Facebook where Google can't crawl. If the Googlebot can't crawl a page, then it never sees the links on that page. If it can't see the link then (technically) Google doesn't even know it exists. The reason Googlebot can't crawl a lot of those pages is because you have to be logged into Facebook to see those pages. And Googlebot can't log into Facebook. It is not a user. It is a bot. It doesn't have an email address and password.