Also Thiel has a history to supporting anti-gay people. Like the anti-gay politicians who get outed, I don't have any sympathy for him and how he has harmed the community.
EDIT
https://www.nytimes.com/2016/10/16/technology/peter-thiel-do...
$1.25M is fairly sizable
2 weeks before the election is timely
For sure Trump is probably indifferent to sexuality, but his voters are not.
Trump is also for X other things one might agree with and Y they might disagree. People vote wholesale, not on individual matters, so other attributes might matter more to Thiel (or any voter). And similarly, X or Y pros or cons on the other side might also matter more (negatively in this case).
Besides, if Trump is indifferent to sexuality, what's the argument? Not to give his supporters (some of which might not be) the pleasure of seeing their candidate becoming president?