Historically, this has happened for a variety of reasons:
  • a deliberate decision to place the center of political power (i.e. the capital) somewhere separate from the center of economic power.
  • as a result of a political compromise. For example, there might be more than one major center (economic or political) and the only way to make them all happy is to place the capital somewhere else (Ottawa and Washington, D.C. are examples of this).
  • reverse discrimination - over time, the effort to prove to voters that the capital isn't getting special favours results in the other center getting a better deal.
  • historical factors which were once critical (e.g. ability to defend the city) but which are ultimately less important than other factors (e.g. transportation) in determining where economic activity becomes centered.
  • changes in borders which result in the old capital being in a different country (Bonn during the cold war would be a classic example).
  • happenstance (i.e. there is no good reason - it just is).
Just for fun (and cuz I'm biased), let's take a look at the Canadian experience*:
  • {British Columbia} Victoria (319,400) vs Vancouver (2,099,400): this is a classic example of changing times. As has been mentioned above, Vancouver barely existed when Victoria became the capital. Unfortunately, Victoria is located on Vancouver Island whereas Vancouver was the western terminus of the first Canadian transcontinental railway. The result was quite inevitable - Vancouver is today one of the three largest cities in Canada and Victoria is a (quite beautiful) sleepy little government town.

  • {Alberta} Edmonton (954,100) vs Calgary (969,600): in the first seventy five years of the province's history (it was founded in 1905), there was no dichotomy in Alberta as Edmonton was both the largest city and the provincial capital. Calgary's position as the economic powerhouse of the province (with a particular emphasis on the oil industry) as led to it becoming (just barely) the largest city in Alberta.

  • {Saskatchewan} Regina (198,300) vs Saskatoon (231,500): Saskatoon has been larger than Regina since the mid-1980s and the gap is increasing. I'm somewhat at a loss to explain what's been happening in Saskatchewan but Saskatoon continues to enjoy steady grown while Regina actually shrank slightly before recovering again in the late 1990s.

  • {Manitoba} Winnipeg (684,300): the capital of Manitoba's history follows the classic pattern of becoming the dominant center early in the area's history and simply maintaining the position of dominance through to the current day (Winnipeg's population in 2001 is over ten times the size of Brandon, the next largest center with a population of 48,000 in 2001).

  • {Ontario} Toronto (4,907,000): like Winnipeg, Toronto established itself as the dominant center in Ontario fairly early and has maintained that position through to the current day. From a different perspective however, Toronto is the victim of a political compromise as the much smaller center of Ottawa, Ontario was chosen as the national capital to avoid having to choose between Ontario's Toronto and Quebec's Montreal.

  • {Quebec} Quebec City (694,000) vs Montreal (3,511,400): Quebec City has been the "political center" of the province of Quebec in many ways since the city's founding in 1608. Montreal, on the other hand, has been a major economic center for about the same period of time.

  • {Prince Edward Island} Charlottetown (32,200**), {Nova Scotia} Halifax (359,100) and {Newfoundland and Labrador} St. John's (176,400): these three cities' histories follow the same pattern of being economically and politically dominant since the earliest days of their respective regions/provinces.

  • {New Brunswick} Fredericton (47,500**) vs St. John (127,300): the capital of New Brunswick was selected and named in 1785 by Thomas Carleton, the first Governor of the newly created province (colony?). The fact that Fredericton was slightly over one hundred miles up the St. John River from the thriving seaport of St. John made the capital considerably more difficult to attack (an important consideration for a region settled in large part by United Empire Loyalists who had fled to the British colony in the wake of the Revolutionary War). The feared invasion never materialized (in any meaningful way) and St. John with a population of 72,000 (2001) continues to be the largest center in New Brunswick. The second largest city is actually Moncton with a population of 59,000. Fredericton is the third largest city with a 2001 population of 47,000.

*the population of each city's metropolitan area, from the 2001 Canadian Census, is given in parentheses after the city's name. The capital is listed first if it isn't also the largest city in the province.
**The population numbers for Fredericton and Charlottetown are for the cities themselves rather than for their metropolitan areas.