If Trump had lost, Thiel would have taken a minor reputational hit based on Trump's pre-election behavior, but since no one thought he would win anyway, it could have been written off as him just taking a chance on an outside candidate. None of the really controversial stuff would have happened, so worst case scenario Thiel looks kind of foolish and wasted a bit of money.
If he had backed Clinton and she won, he would just be one of many Silicon Valley backers, with no particular voice over and above the other billionaires.
But now, Thiel is the only person in Silicon Valley who the President will listen to. That's got to be worth way more than the 1.5 million or whatever that he spent on it.