If Amtrak were adequately funded, they'd have many more options for accomodating all kinds of bikes.
As it stands, they run what they need to run to move people, and no more. Bikes take up space; space has a cost.
On the route I ride regularly, they run a café car on busy holidays; the rest of the time they rely on some dude with a cooler in a corner of one of the passenger cars, because that's what they can afford. A dedicated café car brings with it fuel and maintenance costs that are probably hard to justify otherwise.
Likewise, an open bike policy, bike hooks in every car, a team of baggage handlers at every stop to unload your boxed bike, or even a specialized bike car would be sweet, right? But it won't happen without funding. If you want to start a "letter writing campaign," start with the folks who you elected to help pay the bills for a national passenger train infrastructure, not the train administrators who already know that they can't afford to do this stuff.