As I understand it, by the time it’s going 200mph, the vehicle is completely airborne. It will be flying within the surface effect (ground effect) regime. Striking objects in the water shouldn’t be a problem.
On the other hand, if this is to be a regional solution, then that means passengers might be connecting from a longer flight leg. If you start at SFO in a boat-like airplane, you have a long way to go in the wrong direction before you can soar south over the ocean. The “seaspace” in the channel can be very crowded, and you can’t just go over the traffic.