It's a good question. Particle accelerators rely on firing subatomic particles very long distances with baffling accuracy. And it doesn't take much of a tremble to make the Earth move beyond the tiny margin of such a machine's submillimeter calibration. A quake would barely even have to register to fuck that up, right?
Symmetry, the in-house publication of Fermilab and Stanford's SLAC laboratory, sought out the answer, particularly how it relates to SLAC, which happens to be situated about one kilometer from the San Andreas fault and features a 3-kilometer long tunnel requiring precision down to half the width of a human hair. You know the San Andreas, of course: future site of the "big one," that devastating earthquake expected to upend coastal California pretty much any day now.
So, protecting a delicate scientific instrument is presumably a much different matter than protecting the structural integrity of a bridge or skyscraper or hospital. Turns out the answer, for SLAC at least, is a bit more practical than one might hope for the very archetype of mega-science.
For one thing, SLAC's fault neighbor hasn't been much of a problem.
The most recent event of note was 1989's Loma Prieta quake which, despite packing a punch of 6.9 magnitude on the Richter scale, only unsettled the lab by a couple of centimeters—still enough to require a "lengthy process of going back and putting things back where they needed to be," Scott DeBarger, SLAC's department head of mechanical engineering for accelerators, told Symmetry. The process will be pretty much the same in the event of the Big One: resetting and realigning everything such that the accelerator can again function.
A crucial feature is stiffness, which is what prevents the SLAC tubes from shifting around due to regular day to day vibrations. This is in contrast to the lab's BaBar detector (shut down in 2008), which was even more fragile and constructed to be seismically isolated; thanks to built-in break points in the connections between the detector and surrounding equipment, the detector was assured of remaining stationary should a quake hit.
With a number of nearby faults and a major California earthquake predicted within the next 30 years, SLAC has a response plan in place for when "The Big One" hits.
Should a major earthquake occur, teams will assess the condition of buildings and systems. Then professionals will be brought in to stabilize things and fix what's broken. That's when people like DeBarger will worry about realigning rogue accelerator pieces by asking themselves, "What's its position, and what position does it have to be in to run?
So, the answer is mostly that they survive earthquakes in the same ways as anything else. If a quake hits during beam operation, the accelerator's detectors would register a misalignment and shut down. Moreover, the facility is shielded to prevent radiation from escaping—California will have enough to worry about.