You will also note in the 1952 pictures and documents that the SP line did not, except for the tunnels that actually crossed the fault that moved, experience major damage due to the quakes. Yes, that's plural: there was a mainshock, and many aftershocks including a good-sized one closer to Bakersfield that caused bad enough shaking to pretty much flatten the unreinforced masonry buildings in the downtown area. IIRC the tunnel that got distorted was eventually daylighted; that and some other cleanup took a while (anybody have a good reference for what the work was? Vaguely recall reading somewhere about an interesting shoofly or 2...) but trains were running again within a couple-few weeks. If you want to complain about how the SP line should have avoided faults: it was built in the 1800s when that was not a design criterion; they didn't know about the White Wolf Fault or how active it was until the 1952 quake happened; and even with all that the damage while significant did not destroy the line - it was reopened for limited traffic fairly quickly.

The 1906 quake broke through the SP tunnel between Wrights and Laurel, a short distance inside the Wrights end of the tunnel. SP was running again in a couple of months (there was other damage due to unstable hillsides, too, plus the 1906 quake damaged a lot more than one SP branch line).

BART tunnels through the Hayward Fault. It's a maintenance-intensive spot, because the fault creeps which was not expected when the line was built. Yes, if there's a large earthquake at that spot, it will take a while to clean up and reopen the line; unless other things fall apart though (work is starting soon on an upgrade of the Bay Tube), much of BART is expected to take only minor damage even from a large earthquake on the Hayward (worst case for most of BART).

There are large water tunnels punching through several mountain ranges, including EBMUD & Hetch Hetchy through the Coast Range (EBMUD Claremont Tunnel actually goes through a creeping part of the fault; SF aqueduct crosses the Hayward Fault in surface pipelines with flexible sections in Fremont). LA has tunnels through the San Gabriels. The California Aqueduct goes through the Tehachapis, not too far away from where a Tejon-Tunnels alignment would be for HSR (and like the HSR alignments crosses the San Andreas on the surface for easier repair after a big quake). Would a large quake cutting those aqueducts cause problems? Yes. Temporarily. They're designed so that repairs would mostly be on the surface; tunnels bored through rock, are seldom damaged by earthquake shaking unless the fault actually breaks through the tunnel. LA has several reservoirs on the west side of the fault to help tide things over should there be an interruption, though people might have to stop watering their lawns for a while.

Both the 1971 and 1994 earthquakes in the San Fernando Valley caused considerable damage to railroads and freeways. On the whole, the railroad damaged was cleared up much more quickly (days to weeks), and note that in both of them there was no damage in the SP (now Metrolink) tunnel between the San Fernando Valley and Santa Clarita even though the freeway interchange between 5 and 14 had several bridges go down and in 1971 there was actual ground rupture along the fault not far south of there. Oh yes, peak ground accelerations during the 1994 quake not far from where a train was dumped off the tracks in Northridge were more than 1g both vertical and horizontal (contributed to the derailment?); the line was open again within a couple of weeks. Unless structures go down, it's quicker to repair and restore a railroad than it is to fix a highway.

Bottom line, as Bob said, there are some smart people designing and building major public works and transportation projects. When it comes to details like seismic design, they know what they're doing. While it would be nice to avoid active faults, that's not possible if you want to go from the Bay Area to LA on (or in) the ground. So they design to minimize the damage during a worst-case quake, and make it as easy as possible to fix after one. Just like the Japanese, Spanish, and Chinese (both mainland and Taiwan), all of whom also have major HSR tunnels and earthquake issues (arguably, worse than California's).

There are bigger issues with HSR concept, routing, and design than seismic, really. There's legitimate concern about some of the decisions being made. But engineering for crossing the many faults in California is not something I have a lot of concern about since we now know where most of the potentially ground-breaking ones are.