Raw-food demagoguery never fails to irritate me in the very special way only a neo-luddite fad can.
Richard Wrangham covers most of the reasons in this great TED-style talk. Yes, certain compounds may be degraded by high temperatures, but vastly more nutrients are simultaneously made available for easy digestion (through cell-wall rupture, for instance). The ability to cook food played an integral role in our evolutionary success.
Harvard Thinks Big 2010 - Richard Wrangham - 'Catching Fire: How Cooking Made Us Human' from HTB2 on Vimeo.