F-Stop is both the speed of the lens and the apperature. By speed, it means how much light is allowed through the lens. According to the Lens FAQ:
Q3. What is meant by f-stop?
A. The focal length of the lens divided by the diameter of the aperture (as seen from the front). It is also called an f-number, and is written like f/8, which means the aperture diameter is 1/8th the focal length.
The term is used both in regard to the maximum aperture of a lens and in regard to the aperture selected in a specific situation.
The brightness of the image on the film is inversely proportional to the f-number squared. The depth of field increases but diffraction is worsened when using a large f-number. The effective f-number for all 3 effects changes if the lens is focused extremely close. See Q7.
The term "stops" purportedly comes from old technology in which the aperture was selected by turning a wheel with various sized holes in it, each one of which let in twice the light of the preceding one. Thus the phrase "open up a N stops" means to change to an aperture allowing in 2^N times as much light, and conversely with "stop down N stops".
Glass, even clear glass, will lose some of the light passing through the glass, and some light is lost from reflecting off the glass. A lens is made up of several smaller lenses called elements. Elements always have errors. These erros could be color fringing from refracting the light or straight lines looking warped. To correct these erros usually more elements are added. So with each element you are introducing more light loss, slowing the lens.
Does this mean a 15 element F-3.5 lens is slower than a 9 element F3.5 lens? Is f-stop really a good way to advertise the speed of a lens? Could you have a f-4 lens that performs better in low light than some other f-3.5 lens?