It is mainly about the cost/benefit ratio of making cheap lenses. It doesn't cost a lot more to make a lens f/3.5 than f/8 at an 18mm focal length since the entrance pupil (sometimes referred to as the effective or apparent aperture) is still well within the diameter of the mounting flange used by most interchangeable lens camera systems. As the lens is zoomed out to 55mm, the needed entrance pupil for f/5.6 is just under 10mm while the needed entrance pupil for f/2.8 would be 20mm which is approaching a significant percentage of the diameter of the mounting flange of ≈38mm for the micro 4/3 format or the 44mm of the Nikon F mount. Since most lenses will be made at least the same diameter as the mounting flange, the room for an aperture of the size needed for an f/3.5-5.6 lens in the typical kit lens focal lengths is already inside the lens tube, even with all of the other things that are wedged between the diaphragm and the lens barrel.
Just to check you're talking about the same thing I think you're talking about - according to Wikipedia, the flange for Nikon F is 46.5 mm (Canon EF/EF-S is 44mm). Just a typo?
You are referring to the flange to sensor/film distance, also sometimes referred to as the registration distance. I'm referring to the throat diameter of the flange: how wide the hole in the ring at the front of the light box is, not how far in front of the focal plane it is.