Maybe nobody will commute to Fresno from SF, but I bet there will be people commuting to SJ and SF from Fresno, from Stockton, from SAC etc. From SJ or SF train station they can take the bus or Uber to their work.
Self driving cars still need roads. We are not talking about flying cars. Have you seen how crazy 101 is?
Companies already subsidize their employees on train fares. Even without subsidy the fare forecast published by HSR is not outrageous. We are not talking about people commuting from LA to SF for work everyday. More likely from Stockton to SF or SJ, which many are already doing via cars. These car trips are not free by the way. You pay for the wear and tear of the car, the gas, the hours you put into driving etc.