Candidates A and B are for or against (noted as O and X respectively) the following:

  Issue: A B C D E F G
      A: O O O X X X O
      B: O O X X O O X

Noting that they both agree on three issues, disagree on three issues. I have to weight each of those issues to determine which one I am actually for. While I disagree with Thiel's conclusion this year, I have to presume he's done the same sort of analysis (he's not an idiot, he's well educated and successful so he's done something right along the way). His scales have apparently tipped in strong favor of Trump (especially for him to double down with his donation), but that doesn't mean he specifically supports the more abhorrent parts of Trump's character or campaign.