Well, Thiel himself said that there is something seriously wrong with society if the only people to succeed in building large companies are those whose personality borders on autism. (I believe he wrote that in "Zero To One". If it's not in there, it's in the notes on the lectures which that book was based on.)

So Thiel isn't saying "We are right, society is wrong", which the article seems to imply. Thiel, in fact, is also famous for being able to hold two opposing viewpoints in mind for any given subject. Yes, he makes bets that are very contrarian. But he knows that they are bets, and that he might be wrong. This is very different from someone suffering a Jungian "God Complex" due to reading too much Nietzsche.

(C.G. Jung diagnosed Nietzsche with a God Complex in his lecture on "Thus Spoke Zarathustra". But if you ask people who knew Jung personally, they'll tell you that there was a lot of God Complex going on in Jung's own inner circle in Küsnacht. And Jung also could not know that some of Nietzsche's works had, in fact, been not written by Nietzsche himself, but forged by his sister, who had a self-interest in making Nietzsche's ideas popular with the Nazis. The same probably applies to Rand.)