Thiel has a larger platform for his views than most people, and his success in Silicon Valley is ironically the reason he gets such a platform. He gets blowback because people are listening, and don't like what he says. Everyone's right to free speech is maximized when he says what he thinks and people who disagree with him say what they think.
This article isn't mainly about Thiel. He's in the rare position in that he knows he can live comfortably for the rest of his life even if his employment opportunities are reduced to zero. This article is more about overall atmosphere and culture experienced by standard tech workers. The full excerpt from Tim Ferris (part of which OP's article quoted) really captures this:
> Now, more and more, I feel like it's a Russian nesting doll of facades -- Washington DC with fewer neck ties, where people openly lie to one another out of fear of losing their jobs or being publicly crucified. It's weird, unsettling, and, frankly, really dangerous. There's way too much power here for politeness to be sustainable. If no one feels they can say "Hey, I know it makes everyone uncomfortable, but I think there's a leak in the fuel rods in this nuclear submarine..." we're headed for big trouble.