BART (light rail around SF Bay Area) has interoperated with bicycles very effectively by allowing cyclists to wheel bikes right onto the train in selected areas of the car; Caltrain has a car dedicated to cyclists on each train, with suitable tie-downs and nearby seating so we can keep an eye on our bikes. Most metro bus systems in the area have front-mounted bike racks carrying 2 or 3 bikes.
Amtrak and Greyhound however -- booooo, hissssss -- require bikes to be broken down and boxed for transport as luggage. This strongly discourages use of these two carriers to extend cycling range, except by lucky owners of folding bikes who can disguise them as luggage. In fact my local Hound office will not even let you wheel a bike into the station -- they insist bikes must be left outside, at one of the most theft-ridden bike parking systems in town :-)
Rail systems which allow roll-on bicycle transport with good security, are enormously more attractive than airlines with their $100+ punitive fees for transporting a bicycle and their disassembly and boxing requirements... this is a point on which rail can really get competitive with air...
If bikes are to be left at the station instead of accompanying the traveller, then security is essential: theft is every quoditian cyclist's nightmare, and no one is going to leave a well-loved and/or valuable bike in an insecure location. I have seen some horribly insecure bike parking at many local businesses and the result is, predictably, that cyclists either don't patronise that business or switch to pedestrian or (more likely) automotive travel to go there.
Just a few random thoughts... boy, do I wish we had decent HSR. A good run from San Jose to Seattle on the infamous Coast Starlight is over 24 hours, with the train on sidings making way for fast freights many times during the trip, and average speeds around a pathetic 40 mph. A bad run? could be hours late. Same issues from San Jose/SF to LA/ San Diego: a major urban corridor crying out for high speed interurban express rail, and instead we get one of the slowest trains in the US. I think I've written about the reasons for this "would embarrass a Bulgarian" rail line in a posting long, long ago... The difference between theory and practise in practise ...
That is the best feature of public transportation in California. It should be imported to Europe. Bush is a symptom, not the disease.
On the inter-city electric between Newcastle and Sydney, there were occasional hooks to hang a bike, but the advice was to stay with the bike, and since they were in the entry vestibule, without seating, that would have been an uncomfortable 2+ hour journey. The folder, however, fit in the overhead luggage rack, so I didn't have to worry about it.
Roll-on-roll-off bicycle carriage is an obvious competitive advantage that rail can offer ... but we also have to raise the number of transport cyclists, so that there is a market advantage from being able to offer RORO cycle carriage. I've been accused of being a Marxist, yet while Harpo's my favourite, it's Groucho I'm always quoting. Odd, that.