I find that Metra's current bike policy is difficult to rely on to transport me and my bike, but I wonder if it reflects what they think their ridership wants. If they felt enough of their riders want a better bike policy it would be in their best interest to adopt one.
As for the CTA, I agree with h3. I've never had a problem with the train operators, even when disregarding the rush hour or bike limit per car rules. And I find that bus drivers usually drive with a fair amount of consideration when interacting with me on my bike. But I've also learned to anticipate what they might be doing, and I try to understand that their job isn't easy. If I see someone standing at a bus stop I assume that the bus will be slowing down and pulling over, and I adjust and signal accordingly. And depending on the situation (whether there is a bike lane, the behavior and position of other vehicles, etc.), I'll tend to pull up behind a bus at a stoplight instead of forcing them to hover behind me or try and pass me back three car lengths into the next block.
The blackout dates were posted back in April, 2009. I agree that their notification procedures really do suck when limiting bikes (they really should have posters put up or just signs a few days before blackout times), but the dates are posted well in advance. I put them in my calendar, even though I hardly ride the Metra with a bike.
Trains and buses are meant to move people, not bikes. There's always room for helping Metra understand more that the ridership is growing more interested in taking bikes on trains. However, with the limited capacity of rolling stock, getting more people on the train over bikes is really necessary.
One thing you have to understand about Metra is that it's a railroad. There are hardened people working as conductors who have been freight conductors for years before coming to commuter rail. They may not necessarily see the point of why bikes have to come on trains. I find that it's better to attract bees with honey, and thus I'm very nice to my conductors when I ride the train, thank them, etc. It's not an easy job (although that is not an excuse).
I was not allowed on Metra last week because I didn't not have a chord to bungee my bike with, even though i could see the car was empty on the 12:50 am train.