California is Sacramento; Nevada is Carson City; New York is Albany; etc. None of these are even close to the largest cities for their states. But then in Canada, Toronto is the Capital for Ontario; Quebec is BC; etc., and these are the largest cities in those provinces. So, why are the States so different?
First, in 17 states, the capital is the largest city.
In many cases, the state capital was located to be central to the territory, when the largest city was a port along a coastline edge of the state. In some cases, the capital was established to be apart from—and free of the corrupting influence of—the big port city, or as a compromise between rivals. And in some cases, the capital was the largest city when established, but other cities later grew larger.
I don't see the Canadian experience being much different: Victoria instead of Vancouver; Québec instead of Montréal.