Yes, Virginia, there is a difference.
The word capitol has a very specific meaning. A capitol is the building in which a state legislative body meets, or in which the functions of state government are carried out. When capitalized, the word Capitol refers only to the Washington, DC building in which Congress meets. This probably also holds true outside the United States, but what is important is that these definitions refer to buildings.
The word capital, on the other hand, has many meanings. When used as a noun, it may be the city in which a government's capitol is located, or any city that is the center of a specific activity or industry (the financial capital of the world). Capital may also refer to money, often that used to produce additional wealth, to the uppermost part of a supporting column, and to an uppercase letter. If the word capital is used as an adjective, it may relate to something of high quality (a capital idea) or importance (a capital mistake), or to something involving the death penalty (capital punishment).
The two are not, in fact, interchangeable - while confusing the two is a common mistake, it is still incorrect. While any sufficiently frequent misuse of language may eventually become accepted, it still holds true that capitol refers to buildings and capital is for any other use.