Same-sex civil unions are not the same thing as marriage. Even homosexuals (and homo-friendly judges) consider civil unions inferior to true marriage. As for Massachusetts and Connecticut, which do have court-mandated same-sex marriage, perhaps they are seen as smaller than California, and thus not worth making an example of. After all, Sodom and Gomorrah could not have been the only two immoral places in the world at the time they were “zapped.”
Also, those two states only legalized it for their citizens, barring people from other states from coming in, getting married and then returning to their own states. California did not have this provision, which meant that people could come from other states, get married and then return to their own state and demand that their California "marriage" be recognized under the federal Constitution.
I don't know if the fires were a warning, but I do believe that God is slow to anger. As Father Corapi has said, we cannot depend on Him staying His anger forever as we continually reject His eternal truths. Especially regarding homosexuality and abortion.