From what I know it's because most Americans don't like the French. So instead of calling them "French fries" (although French fries were not invented in France) we called them Freedom fries. The name was changed as part of an idiotic propaganda campaign.
Fries were always called French fries in America. until George Bush decided that it was necessary to attack Iraq. He attempted to enlist the aid of the United nations in this adventure. The French did not want the UN to be involved in a war of aggression and voted against the proposal. American interests were so annoyed by this that they changed the name of French Fries to freedom fries in protest. So besides not becoming involved in a pointless war the French also got a good laugh out of it.