I paint bicycles for a living, and believe me, matte is a drag. By nature, it is porous (much like sanding primer). So it will absorb oils and grease, which is why it darkens and stains so easily. Once those oils are absorbed, they are very difficult (if not altogether impossible) to get out.
The matte finish is created by having a film of 'matting agent' deposited on the surface of the clear coat during the drying and curing process. The evaporating solvents in the clear bring the matting agent to the surface s they are escaping and evaporating, giving you that matte effect. Problem is, it's really only on the surface, and what's below is normal clear coat. This is why your matte finish gets incrementally more shiny the more you rub on it. You're removing the thin layer of matting agent and exposing the gloss clear underneath.
Durability of a matte finish isn't the same as a gloss finish, but it's not terrible. Matte finishes need to be sprayed a little thinner than a gloss clear (laying on too heavy a coat traps those carrier solvents in leaving you with a shinier surface than you had planned on), giving you less film build and, therefore, less protection. I'm sure Trek's finish is superior to most refinish materials (I use PPG), and may last longer, but I would never want a matte finish, and I don't like doing them for customers for the reasons outlined above.