The tube might keep the train from flying off the tracks, but will possibly lose vaccuum. But maybe not. The trans-Alaska pipeline crosses the Denali fault, which is a big strike-slip fault similar to the San Andreas. The pipleline is on rail-mounted pylons that allow for several meters of lateral motion near the fault. The fault had a M 7.9 earthquake in 2002, and the pylons slid as intended, bending but not breaking the pipeline[1].

Now, I don't know that much about the Hyperloop design, but I imagine that the earthquake-induced deflection in the tube may render it unusable for some amount of time. However, the the example goes to show that somewhat similar infrastructure can be built to withstand large seismic events, as long as the faults are known about ahead of time (which is the case in southern California but not everywhere on earth).

[1]: http://pubs.usgs.gov/fs/2003/fs014-03/pipeline.html