several reasons, ranging from marketing to the consumer, to actual practicality for the average consumer.
to begin with, the specktra-mua-and-LJ-addicted mac users are far and wide outnumbered by the average consumers who don't spend as much time reading up on the MAC product spectrum. many are unaware that mac pigments even exist, as they are not widely available at all mac counters. most tend to buy pressed eyeshadow pans, as they are easier to use, easier to travel with, and, for the most part, are believed to be "quicker". mac has several matte shades as parts of their regular eyeshadow line. if a customer wants a matte color, they will probaby purchase a matte shadow pot.
also, on the rare occasion that counters do get pigments (for example, with the LE lines), they want items that are flashy, and that catch the eye easily. if the average shopper is walking through a nordstroms, for example, and pass by the MAC counter, MAC wants to make sure that the products on display have maximum potential, and therefore, are an easier sell. shimmer catches the eye, and it is much easier to convince a customer to buy a loose, shimmery pigment for the eyes, purely because most people have more experience with shadows with shimmer. it's all about making the maximum amount of revenue. they figure that those with enough expertise and knowledge of makeup to actually want matte can go to the pro store, or find other means, of purchasing the matte pigments.
i personally like the matte pigments, and find them decently simple to use, providing you use the right brushes, the right technique, and start with a little product, building up the color as you want. still, most of my friends who aren't mac-addicts tend to shy away from my mac pigments.
i can see why they are not offered at regular freestanding stores, because i have a feeling if they were, they'd get a LOT of customer returns on them. products can seem so appealing when you are shown by a makeup artist, yet seem so difficult when you bring them home and try them yourself. i have a feeling that matte pigments might potentially cause this reaction.