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You are right that a normal optical instrument has only one focal length. But here, you look at a combination of a lense and(!) a sensor that consist of a 2d-array of detectors (formerly known as pixels). Your focal length therefore has the unit meters/px. If your camera's pixel pattern is a perfect square, fx equals fy. If the pixels are a bit rectangular and not quadratic, fx differs from fy. This effect can be captured by using two different focal lengths.
There is even a version of the intrinsic calibration where there is a skew value that incorporates an angle between the rows and columns of your pixel array that is not 90deg.
