A small group of protesters were calling attention to a company he co-founded called Palantir.
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Thiel is one of only a few Silicon Valley giants who supported Donald Trump for president.
Former San Francisco City Supervisor Dave Campos says Palantir won a contract to do work for the Immigration and Custom's Enforcement Agency.
"They've received this contract, which will essentially create a data system that will allow, that will enable the mass deportation of millions of people," Campos said.
According to the federal government, in 2014 Palantir was awarded a $41.6 million contract to create an ICE investigative case management system.
Privacy advocates fear the Trump administration could use the system to mine big data to track immigrants as they travel.
They say algorithms could flag someone because of a meal request on an international flight.
"Where is everyone in the country who has ever asked for a halal meal on their flight? What are their names? Who do they associate with?" Privacy advocate Edward Hasbrouck said.
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Trump sparked massive protests and chaos for many travelers when he issued an executive order creating a travel ban aimed at seven primarily Muslim countries.
These advocates worry these tools could also be used on citizens.
Not everyone at the protest opposes Thiel. "This may be a little controversial to say, but I think Thiel has thought a lot about civil liberties given his background as a libertarian," demonstrator Michael Tsi said.
He hopes the tech mogul will bill safeguards into this system.
Our sister station, KGO, reached out to Plantir, but has not received a response.