It may be a detour, but transcontinental rail is essentially just for tourism at this point. If someone wanted to get from Halifax to Vancouver, they probably aren't taking the train.
With that in mind, it's much less important for the route to be direct and much more important that it connect important tourism hubs. As such, Toronto's role as Canada's main air hub makes it an important end point for people who are, say, flying in to Vancouver, taking the train for the experience, and then flying back out of Toronto.
That said, I think it would be really cool to have a Halifax-Vancouver train - the first
true Atlantic-to-Pacific transcontinental and a full week of travel