Boy, you Californians never give up! The Left Coast must be the last place in the nation where people are as giddy with delight at the prospect of sitting behind a steering wheel as folks elsewhere were in, say, 1950.
In any event, comparing rail vs. auto commuting is much the same as debating whether it's preferable to be electrocuted or gassed -- neither alternative is that great. All in all, though, I think commuting to Manhattan via the LIRR is slightly less shitty than traveling by car because you can at least read on the train, so the time isn't completely wasted.
Carl