it wouldn't be a highway, it's called an overpass. and they're quite common.

Rivers have limited bridges. I live in a city divided by a river (I suspect a large number of those reading this do as well: rivers attract cities for various reasons), most streets just end at the river even though both sides are very developed. If I want to cross the river there is are 5 bridges in the 15 miles of river frontage the city covers (then nothing for many more miles either way). There is great demand to get across the river, we are a tiny city and so the only traffic congestion is getting to the river crossing, but the cost of getting over the river is high enough nobody can justify building another bridge.

I don't know SF, but my guess is that market street will have more crossing than our rivers.