I suppose my confusion came from doing a quick web search to find out what was meant by "safe space."  The first thing that came up was a Wikipedia article that says;

 "In educational institutions, safe-space (or safe space), safer-space, and positive space are terms used to indicate that a teacher, educational institution or student body does not tolerate anti-LGBT violence, harassment or hate speech, but rather is open and accepting, thereby creating a safe place for lesbian, gay, bisexual, transgender, and all students."

The easy jump from there is to ask who is harmed by allowing intolerance, and why would they be so concerned about a newspaper comments section?  I'm afraid the answer to that question is rather ugly.

If, as you suggest, the term has come to mean an exclusion of topics or ideas on a larger scale then that is something different.