The bottom line is that Thiel believes the 'positives' of a Trump presidency would outweigh the negatives.
The expected value is positive versus a status quo Clinton administration so he should support Trump.
He lays his priority set out quite clearly in his RNC speech: http://time.com/4417679/republican-convention-peter-thiel-tr... and if you agree with his central premises of a structurally broken economy, excessive foreign intervention etc then tbh Trump is the only viable candidate even after recent headlines, particularly if you believe in the strength of US institutions to curb any excesses.
If Thiel's position were based on hatred then I think it would be another story, but as it is, again given acceptance of the possibility of his central premises being correct and Trump being a 'viable' (as in could win vs Stein or Johnson) major party candidate his support is rational.
Across America Trump will win fifty million votes or more and while some of them may be deplorables voting for deplorable reasons, many will be voting based on implicit expected value metrics.