Look at the brakes on a motorcycle -- you effectively have only 1 brake. (okay its really like 1.25 or so, but you know what I mean). That 1 brake has to do its work in all conditions and with 100% reliability. If it fails in any way you're toast, butter side down. This means the part has to be manufactured with the highest grade materials, with the closest tolerances and the lowest attainable level of manufacturing defects. If not someone will die. Furthermore that brake is expected to perform at the highest levels. A modern bike is expected to perform like an exotic sports car. On the power side that's fairly easy -- make more of it. On the braking side, it means you have to build high quality brakes. That's just expensive. You can't use just any ol' press to put the floating bushings in, its got to be a press with high accuracy and tight tolerances. If you made the rotor by hand, you couldn't just use cheap labor to turn the thing on a lathe, you need a highly skilled professional machinist to turn the thing out properly. On top of all that, weight is an important factor too -- you don't want just any old hunk of iron, but something that is relatively lightweight and strong and that's not cheap. And then, you are only going to make a few thousand of them meaning the investment in this high quality machinery or labor and materials has to be recouped in only a few thousand units while making a profit.
Now compare that to a car. Here you've got 4 brakes. If one fails its not catastrophic. It might be bad, but not the instant disaster that a failed motorcycle brake creates. That brake is NOT expected to perform at the same level as a motorcycle brake, generally speaking. Add in things like ABS and the actual required quality of the brakes probably goes down even more as the technology can compensate somewhat. So that means the part can be manufactured with lower tolerances and out of lower grade materials. Then scale that up to a manufacturing run an order of magnitude or more higher than that for a motorcycle... then multiply that number by 4 (4 brakes on a car, remember?) and you'll see that it makes sense. Lower infrastructure and manufacturing costs coupled with dramatically higher volume gets you cheap prices.
For a valid comparison of brake parts costs, compare the motorcycle parts to something more equivalent -- maybe the rotors for a 350z (or whatever they are now), rx7 (8?), 'vette, whatever, but a car that has similar production runs and similar performance characteristics and I guarantee you it will be a spendy little bit of metal.
Now having said all that, if I were making motorcycles, I'd use off the shelf parts, or parts that were the same across lines (I imagine they do this anyway) to realise some economies of SCALE, though you can't really get much in the way of economies of materials and manufacturing costs due to tolerance levels. So there should be some price break at some point. I don't doubt that likely the manufacturers and definitely the dealers are taking a nice tidy markup, but that is not the sole cause of the problem.