Well, the Kilrathi have (or had, anyway) more resources on their hands. After all, they DO have a gigantic system-spanning empire, and the Confederation, while large, is definetly NOT an empire. Besides, they have to go through all sorts of bureaucracy before they get their ships online (case in point: Action Stations and the Prophecy manual, where well-intentioned senators strip Confed). And the Kilrathi, being the bad guys, don't have to worry about being ethical; they could be using massive slave labor or strip-mining planets,, for all we know!
Besides, size is not always representative of power and/or resources; I mean, look at the gigantic Yamato battleships that Japan put out during World War II. Big, powerful dreadnoughts, twice the size of the US Iowa class, capable of taking out any ship in one-on one combat (and maybe even four-on-one).
But, as Bandit LOAF said, CARRIERS don't fight one-on-one, and when the Americans ran into the Yamato, they swarmed her with carrier torpedo bombers. Lacking fighter cover and virtually alone, she went under. As Admiral Yamamoto knew, what Japan really needed was carriers; by building the Yamato, they drained their limited resources, resources that could have gone to creating more carriers, planes, and pilots. The Yamato, like the Dreadnought, is a large, powerful symbol of brute strength, but little else.