You're getting at the heart of the matter as far as the complexity, but just to put an even finer point on the it:
A single gene sequence can code for many different alternate versions of the same protein. These different variations can have pretty wildly different biochemical properties. Furthermore, the protein products of a given gene varies by environment, ethnicity, organ, tissue, cell type, and stage of life (development, infancy, puberty, etc...).
If that weren't daunting enough, many proteins have a secondary function of regulating their own production and the production of other (somehow related) proteins. This means that there are these highly complex interdependent feedback loops governing the activity and concentration of proteins.
The closest programming analogy might be spaghetti of LISP-like macros that are themselves spaghetti code that writes LISP-like macros.
But all that covers the basic research question of "how is this gene connected to human disease?". Even when you get past that, it's not so easy to know what results to supply back to patients. Do you tell the parents of an 8 year old who has had her genome sequenced that their daughter has a very high predisposition of getting cancer in her 40's? The daughter is too young to consent to hear that info. Now you're forcing the parents to make the choice for her. Not only that, even though the child is the one in for the test, the parents now (possibly without fully thinking it through) are recipients of information about themselves. All that because they wanted a genetic test to see why she's shorter than average.