Tunnel through a fault line? Sure, it's done all the time. The bigger and more active the fault, the less you want to do it of course. And the "ground" in the fault zone tends to be really hard to work with and is often full of water. Question is: how active is the fault, and how soon after it moves do you want to be able to start operating again? Also: what kind of fault is it?

BART runs through the Hayward Fault between Rockridge and Orinda. If you look carefully, you'll see a section of tunnel that's wider than the rest - so if the fault moves only a few feet the track can be picked up and realigned to get back into operation quickly. Hayward Fault usually moves sideways - little vertical or compression movement. Not sure if the "patch" operation there would work if a big one happens, though, because fault movement in one of those on the Hayward could be 10 feet or more; that would probably require a substantial bit of new tunnel.

San Andreas is the kind of fault you want to cross on the surface, which is what HSR (even the now-dead Grapevine tunnel alternative) and most of the aqueducts do. It doesn't move often (except in the Hollister area where it's always creeping), but when it does it's big - 10-30 feet. You need surface access to fix something after that kind of movement.

There are fault zones at the northern base of and elsewhere in the Tehachapis that have compression and vertical movement. The ones at the northern base of the mountains are very active, though they don't do anything big very often (1952 a major exception). The result is slow ground deformation, such as around Wheeler Ridge, and the occasional quake big enough to cause some damage. In 1952, the Tehachapi line was closed for a while due to collapsed and compressed tunnels, including some where the rails were bent into a loop and shoved under the tunnel wall. Similar thing happened 1906 in the Santa Cruz Mountains where the Wrights-Laurel tunnel crossed the San Andreas; unlike most other spots along the S.A., there's compression in that area. And similar faults are active (1971 for example) at the north end of the San Fernando Valley.

Bottom line: you can tunnel through a fault. You need to know what you're doing. And if it's a major or active fault you probably don't want to do it if it can be avoided - the damage is easier to fix on the surface after the fault moves.

Trivia question: where do rail lines presently cross or run within the San Andreas Fault zone? Hint: all but 2 are on UP, and 1 includes both UP and BNSF.