Programmers are unique in the world, in a philosophical sense, in that the skills and techniques of programming can be applied to any human subject, and seriously productive results can be attained. Computers are an "infinity machine" in that any single subject that a human being can describe, using words, can be in some way supported by computerization.
So if you think an organization is broken, programming can often-times fix it. Good programming, which encodes the domain-specific knowledge of the organization, can be applied to any particular role in human existence - including that of management. In that sense, programmers are able to operate exterior to any organization - and must, in fact, if they wish to deliver a productive result - and apply their skills to that organization in order to improve it.
Programmers who have worked professionally in any industry have an intuitive understanding of this fact, and its strengths.
So I would put it to you that its not Stockholm Syndrome you're observing, but rather this simple fact: Programmers > Managers. (Well, Programmers who deliver working systems, that is..)