Thiel is a libertarian. If you're up for reading... http://unqualified-reservations.blogspot.com/2007/12/why-i-a... dives into some differences. The key one IMO being that no neoreactionary should actually vote. Trump is of course the obvious best candidate from one branch of the NRx perspective, but him taking office doesn't fundamentally change things. Another branch of NRx could argue Hillary is the "best", too, but the reasoning may be surprising.
The underlying reason for which I think Thiel might support Trump is that Trump is ultimately a businessman, like Thiel, and one in the messy business of real estate development at that. (For a fun fairly anti-Trump piece that could also read as support: http://slatestarcodex.com/2016/03/19/book-review-the-art-of-...) A common NRx thread is that pretty much any chief executive (which includes military generals) would do a better job at being President (and even better King) than the more traditional list of possibilities like lawyers and professors.