Thanks to all on this thread. It really improved our transportation links page related to public transit from Bay Area to Yosemite.
But out-of-staters could also consider the option Roleigh proposed - fly to Fresno via LAX, overnight there, then early morning Amtrak train and YARTS bus to Yosemite.
All this (including Roleigh's thought) are athttp://groups.yahoo.com/group/johnmuirtrail/links/Transportation_001262977366/
While Fresno also usually will require an overnight hotel stay, Fresno probably has cheaper hotel options than SF, and it gets you to Yosemite earlier in the day.
From some places you might be able to get a redeye flight into one of the available airports (SFO, OAK, SAC, FAT) early enough to catch the morning train. For most people, however, it's probably one day for air travel, a hotel overnight, then next day starting early on train-bus of bus-train-bus to arrive Yosemite either side of the noon hour.
John Curran Ladd
1616 Castro Street
San Francisco, CA 94114-3707