Which is a valid complaint given the nature of Skype. There's also tons of other reasons, though. Primarily technical ones.
Either way, software freedom is an important goal and even though I don't necessarily agree with RMS in this case, I understand where he's coming from. So many people seem to have some phobia of accentuating the ethical, freedom and community contexts that the term "free software" implies, preferring the more bitterly pragmatic "open source".
That and this is a very typical RMS rant. This is probably the umpteenth one of the same variation, only with $SOFTWARE being Clang/LLVM in this case.
For the record, I love Clang/LLVM and support BSD licensing. For a lot of software, having an open source development model without the deeper freedom contexts is good enough.