Crossfit started out as regular old "Cross training" (look up John Jesse's training or Bob Gadja's PHA training for a very similar type of training) with some hip marketing behind it to market it to yuppies. It also helped that it was getting popular as people were tiring of the specialization fitness programs, and older fitness ideas were becoming popular again(Olympic lifting, bodyweight training, Kettlebells, etc......).
With Crossfit, it really depends on who's designing the training. There are, and were, some smart folks attached to it, but as it became popular the level of programming went down. It slowly turned turned into "How can I get the most training done in the shortest amount of time" rather than smart training. The fellas that questioned it were either stifled by corporate or left on their own.
Some also stayed for the Crossfit branding because it brings in the cash, but moved toward their own style of traing with a few Crossfit principles thrown in. These are the one's that actually do the best. Very few actually follow the traditional Crossfit main page workouts that the public see.