I guess (my opinion) they don't realize that a major US highway goes through there and sometimes people need to go through SF.
The Central Freeway is not even the best way to go through SF if that's what you're trying to do. East Bay <=> Peninsula is already covered by a freeway route, and Marin <=> Peninsula traffic is using CA-1 (which, if anything, could be a candidate for a better/faster route). Long-distance traffic isn't going straight through SF, either.
Otherwise, it's a stub freeway. You're already going to be on surface streets to get to where you're going, likely several miles of them. A few more blocks is not likely to make a big difference.
What is a concern is that SF is so gotdam expensive to live in that people practically have to commute in from Wendover, Utah to be able to afford to work there.
That is true, but the highest-paying jobs are based out of places like Mountain View and Menlo Park that have plenty of freeways....
We forgot about the most important question, though: if this happens, what happens to the route designations?!?!