Its a numbers issue. High speed rail in the Toronto-Ottawa-Montreal corridor would cost $20B or so, give or take. At a cost of capital of 8%, that's $1.6B/year that could be spent on, among other things, a fleet of A320 aircraft (figure $50M/each).
When you look at VIA's numbers based on their load factor, they really aren't all that much more energy efficient than flying (and actually quite worse than flying if you benchmark against the long-haul trains!). "High speed" rail would be even less energy efficient on account of the higher speeds and higher inputs to track maintenance/construction. Airlines like AC and WS cover all of their costs (short and long-term) with fares they charge. VIA covers only a fraction, and that's not even with proper long-term amortization of their capital infrastructure.
I like VIA (minus the delays, the severely out of date equipment and the often highly demotivated staff), but its existence makes very little sense to me from a dollars and cents point of view.
BTW, if you ever get the chance, take the Jasper-Prince Rupert trip. The scenery is to die for.