There's no way to know, but my guess is that had Thiel stepped up in public a few years ago and said, "Gawker is a terrible gossip rag that needs to be taught a lesson -- contact me if they've wronged you too, and I'll help you mount a case", people would be less angry at him.

People don't like the idea that a shadowy cabal can run things behind the scenes without any public scrutiny.

Secondly, the ACLU does not generally appear vindictive. The ACLU looks to fund cases with a motive that people generally understand to be making things better for American society. Thiel may claim that removing Gawker from the face of the earth is a public service, but given the obvious history, that seems laughable. He appears vindictive, not altruistic.