Having traveled several times with a bike on Amtrak, I would like to offer a helpful hint. This applies to the Downeaster and the Northeast Regional trains, which share the same carry-on bike hangers. It may also apply more broadly to other Amtrak lines.
The bike hangers are designed to hang a bike by the rear wheel. Amtrak says the bike rack hooks will accommodate tires up to 2" wide. While that's true, it is only part of the story. The hook is shown here:
The other key dimension is the depth of the tire+rim, since the hook needs to pass over both of these in order to hang the bike. The system is not designed for deep-section rims. To fit through the hook opening, the tire+rim need to be less than 75 mm or 3 inches. Here is an example:
This tire/rim combination just barely squeezes through the hook opening. if your bike has a taller tire+rim height, it will not fit on the hook! I have heard stories of bikes being refused because they could not be hung properly. On the other hand, I was once allowed to park my bike in the wheelchair area next to the bike closet. So it may depend on the situation and your conductor.
My bike is extra-tall so, when hung, the saddle sticks out into the aisle. To give passengers more room to walk by, I pull the saddle and seatpost out.
In my experience, fenders and aero bars do not cause any problems with the bike hangers.
I like traveling by train with a bike. Amtrak is slowly becoming more accommodating towards bikes, which we should all cheer.
Eric N