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I've been using Uber for the past few days and it works great. I've also talked to the drivers in my admittedly limited Spanish and none of them reported any safety concerns. Also talked to other tourists and none of them had issues using Uber.
So the answer as of December 2019 is that it's perfectly safe to use. Although do note that it officially remains unlicensed within the state of Baja California Sur, similar to many other jurisdictions where Uber operates semi-illicitly.