I know it's an old thread but it did pop up when I searched for VIA Rail. I've been researching VIA for bike outings around Toronto and they don't go out of their way to be helpful! I'd be interested if [MENTION=156952]Doug64[/MENTION] 's trip worked out.
My understanding is that you need to be sure the train has a baggage car, and then check if the baggage car has a bike rack. If it has a bike rack, you can walk your fully assembled bike onto the platform to be loaded. If it has a baggage car but no bike rack, you have to check your bike, buy a box from them, remove the pedals and turn the handlebars.
At least that is what I have gleaned from the website.