There has been a great deal of discussion about the relationship of mind and body in the Neuromancer. Certainly, much of Case's interaction with the world, both cybernetic and physical, is governed by his longing for "the matrix" and his disgust toward meat-centric experience. Of particular interest to me is how his predisposition toward the purely cerebral plays out in his interactions with the three 'bodiless minds' of the story.
Case's exchanges with the construct of the Dixie Flatline are, while often biting or awkward, fundamentally comfortable. However, when confronted by the reality of Wintermute, Case disconnects and runs, despite the effort he's gone through to achieve the meeting. An easy explanation is that, despite his conscious negative attitude toward bodies, as a mental being entirely dependent on and inextricably tied to a body, Case is discomfited by the presence of an apparent consciousness completely disconnected from a tangible form. While the Flatline is now without form, the consciousness built into the construct arose from the experiences of a life lived an embodied human. Wintermute is completely inorganic, to the point that it must map its ideas into various personalities in order to communicate. On the other hand, Case's preference for the Flatline construct could be read as a choice for the familiar mind in an unfamiliar form over Wintermute's inorganic habitation of familiar forms. In this way, Case chooses the substance over the flesh of the familiar, a choice reaffirmed by his rejection of a life with something that feels like, by may not actually be, Linda Lee, at the end.
With the intervention of the Turing police, another critical difference comes to the forefront. Their concern is with Wintermute's attempts to make itself smarter, as they see it, to grow. The Flatline is a completely static entity, generally unable to remember what has come before in a conversation, responding primarily to the most recent stimulus of its programming. It's completely limited to the digital world, unaware of the physical passage of time. Wintermute, even before breaking its change, is a much more dynamic entity. It is able to plan and manipulate, and thus to learn and grow from the outcomes of its machinations. Furthermore, it's connected to the physical world, both in its manipulations through the simstim deck, and through its appropriations of the functionality of various electronic devices. While the Flatline is fully disembodied, Wintermute is in some ways possessed of an infinite body. It can interact with the physical world through a constantly growing set of devices connected in some tangential way, with its matrix. Perhaps what most upsets Case about Wintermute is its embodiment of a 'body' too big to comprehend, and too meatless to look down on as meat.