Depends on the jet.
Jet planes can drive along a highway, but they make for poor tow trucks.
That crash looks like a relatively low-speed one. A ship falling all the way from space would probably create a drastically different-looking impact mark in reality, but we can forgive Hollywood for that. Yet a ship falling from space would be unlikely to hit San Francisco Bay rather than some other random area of the Pacific or of dry Californian land. Do starships in nuTrek regularly operate from the surface of Earth, perhaps?
I would guess so, primarily because that's a trope that's become more and more common in sci-fi these days.
In-universe, though, there's something to be said for your ability to extend your shields around the city you're protecting, use your phasers to intercept incoming missiles and torpedoes, quickly beam/shuttle people and equipment to and from the surface without having to worry about orbital positions and travel times and so on.
Of course, there's also the fact that San Francisco is supposedly the home of a major shipyard, so this could be interpreted as a starship getting suckerpunched by the bad guys just as it begins to take off for its maiden voyage.