In terms of legitimately using a bike for transportation, the same challenges come up for everyone. The biggest obstacle, particularly in the U.S. has to do with the sheer scale of urban sprawl. I originate in Dallas, one of the largest metroplexes nationwide. It takes 2 hours to cross, in good traffic, on the freeway. Austin, while substantially smaller, suffers from the same syndrome. As did the Bay Area during my tenure as a resident of Silicon Valley.
So the solution for many (myself included) as one who is alternatively transported, is to mix my modes of transportation. My favorite combination is the MetroRail/Bike combo, which I have used in the last 3 cities I've lived in. A few examples:
Here's Grey Bike a couple years ago, loaded down and waiting for the train to transport me and my stuff home. In those bags are lots, and lots of brewing supplies which sort of destabilized the bike, so I elected to let CalTrain do the work for me.
More recently, this is the Surly waiting at a CapMetro Rail station for the train to come and ferry us to downtown to watch a movie. The ability to put my bike on a train has a powerful influence on where I will go, when, and probably most importantly with destination-oriented cycling, how I will look and feel upon my arrival. Maybe it's vain, but it's important to me. I hate drinking and driving, but I also hate looking like a sweaty ragamuffin.
So a hybrid approach is called for. Train accommodations for bikes vary from negligible to quite nice, depending on who designed the train you're riding. Having taken a bike on 3 rail systems in 3 separate cities at this point, I feel I can say CalTrain had the best accommodations - an entire car that was nothing but racks for bikes, with a capacity of 16 bikes (4 racks per car, 4 bikes per rack). And they filled it, every day. They turned people away some mornings because the trains were at or over bike capacity.
The issue in this country with making public transportation comes back to urban sprawl. The issue, as it's known among cycling advocates, is of "last mile" transportation. See, the thing about public transport is unless you're very lucky, or live somewhere very dense with a very comprehensive system, public transport rarely puts you precisely at your final destination - sometimes you have as much as an additional mile or two to go. So how to surmount the last stretch? The bike is basically ideal - light enough to be portable, quick enough to be practical. But without good facilities, that last mile become a substantial barrier to making rail systems jive in a country that's cities are defined by their sheer scale.
Ever tried the mixed method? Thoughts?