As the NBC Bay Area story points out, there have been hardly any requests for Clipper card data, because that requires a search warrant or subpeona while the cops can easily get cell phone tracking information without jumping through those hoops (thanks to some very bad court decisions). So if they can track your exact location via your phone, they don't need to care which bus or train you rode on.
So unless you don't have a cell phone, you really have little to worry about from Clipper cards.
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