First, the police have a weird habit of determining that black people drive the most suspicious cars. Does this racial profiling extend to their drone use as well? It's clear from the article that the police are using the drones in more situations than just the active investigations that they claim to use them in. (https://en.wikipedia.org/wiki/Driving_while_black)
Second, if you're being followed by a police car, you know the police car is there. If you're being followed by a drone, you have no idea the drone is there. From the article, the SFPD's drone policy states that operators must only record video once the drone has arrived at the scene, and they must take care not to record individuals unrelated to the active investigation. However, every video had recorded the full takeoff, flight, loitering, return flight and landing – capturing all of the people in SF going about their daily lives. One of the videos showed the drone hovering outside the windows of an apartment building while police schlepped around inside; if I lived there, would I have to worry about a drone appearing outside my window and recording me jerking it in the privacy of my own home? Would I even know it's a police drone, and would I be able to guarantee that the footage was deleted?
Third, I can pull over and ask the cop why they're following me, or (more likely) just let them pass. A drone is just going to loiter there, waiting for me to commit whatever crime they think I'm committing.
Finally, I hate to invoke the slippery slope argument here, but IMO it's warranted. It's easy to deploy drones wherever you want throughout the city; it's not easy to tail every vehicle waiting for them to commit a crime, just because you find them suspicious. If police find drones to be super effective at tailing all of the people they want to tail, why not buy more drones and just have them hover throughout the city perpetually so there isn't a square inch that goes unwatched?