They may be charging a lot, but that does not make it a nice neighborhood. But I guess they figured they could fleece people who did not know their way around the city.
Downtown SF has always been a soulless wasteland for the homeless and people who do not actually live in the city. Life in SF has always been about the neighborhoods. So basically anything West of Van Ness, South of 16th, and North of Broadway (with the exception of Nob Hill) modulo the character of the neighborhood.
The trick with muni busses is to always sit by the second set of doors. Crazy people ride in the front. Thugs and teenagers in the back. Normal people in the middle. The muni rail is truly an abomination. But the daily game of sardines is part of the charm … I guess