I think the issue that people have with Thiel supporting Trump is that if America needs an anti-establishment president to "shake up the system" that is not Clinton/Romney/Ryan/etc, then it's hard to believe that Trump--with all his flaws--is the best choice. You're telling me there is no one better that Thiel can throw his support and money towards? I find that hard to believe.
I guess some people just like to watch the world burn.