I completely agree with Neil Ward-Dutton when he argues that Businesses aren't machines, and enterprise architecture can't make them so. There is a fantasy that Enterprise Architects are architecting the enterprise, when they are at best architecting systems of systems to support the enterprise.
The people who are really making structural decisions about the business organization itself are not called enterprise architects, they are called CEOs or COOs or something like that. And you can bet they aren't playing Zachman bingo.
Neil and I agree about a lot of things, but one of the things we disagree about is the word "alignment". (See previous debate on Business-IT Alignment). I think this word completely misrepresents the relationship between IT and business, and I think Neil's argument here just reinforces my opinion on this.
But the image of a business as a machine is a powerful one, not restricted to enterprise architects. Gareth Morgan devotes the second chapter of his modern classic Images of Organization to this metaphor, and to showing the limitations of this bureaucratic view. (Essential reading for enterprise architects.)