Well, part of the reason right now must be the lack of supply and the greater demand, which always jacks up prices. If they're also more expensive normally, it's probably because they don't benefit from the "economies of scale" that calibers such as 9mm, .40 S&W, and .45 ACP do. These service calibers are used heavily by the military, police, competitive shooters, and a large percentage of gun enthusiasts who shoot regularly for practice and for fun. Since their production is always fairly high, there is a lot of production capacity and components are produced in massive quantities, allowing for the most efficient methods to be used. Even though demand for them is usually also high, prices are kept as low as possible in order to encourage the market to grow or at least retain its consumers (as we all know, shooting can get expensive real fast).
Other calibers might be used heavily by some people, but the volume is still much lower overall (except for .22 LR, obviously), despite the majority of guns being chambered in the smaller calibers. The vast majority of people who own these guns, not counting those who are gun enthusiasts, simply don't shoot them much (when they do, unfortunately it's usually for a serious reason, righteous or otherwise). While lower demand usually means lower prices, in this case the cost of things like shipping, packaging, and even retail shelf space forces prices up to make the ammo worthwhile to produce in relatively small quantities and keep in stock. Perhaps an expert in manufacturing can give you more details about economies of scale, but in general lower volume production is less efficient and therefore more costly.