Because, as arethuza said, programmers don't have the tools that other engineering disciplines have. Most notably, the equations that allow for predictive analysis and proofs of correctness.
A civil engineer that builds a bridge can be fairly certain it won't fall down even when it's still on paper, because he can reason about the forces and stresses and even environmental degradation via well known equations and models. This collection of predictive and proof techniques is what makes it an engineering discipline.
Programming doesn't have that, at least not yet. As you point out, the program is the input to the machine, not the predictive model. But at least if the machine acts deterministically, we can focus on proving things about its input, the program. There has been quite a bit of effort in the research community to come up with ways to prove correctness, but the state of the art is still a long ways from being something actually useful. Functional languages are (partially) a reaction to the prediction requirement. By not having side effects or depending on state, it's easier to make predictions about behavior. (Of course, lazy evaluation buys you a lot in expressive power and data structure efficiency, but offers a new hurdle in predicting performance).
And if you really look at it, Software Engineering is, well, not. Everything I have seen in the emerging Software Engineering field is really about managing people. It's about how to get 1000 developers on the same page (which is like herding cats) so they can crank out an operating system. Sure, there is a lot about testing and validation and change control, but it's still mostly from the angle of controlling the risk of a developer doing something stupid. The tools that would allow a software architect to write an exact specification of a project (bridge blueprints), prove it'll meet all requirements (not fall down), then turn it over to junior programmers (construction crew), just don't exist yet. Check out Rosetta for an ongoing attempt.
So maybe someday programming truly will be an engineering discipline, but right now it's more like having a million Wright brothers all building their own airplane, using whatever materials they are used to working with, rather than an established discipline like Aeronautical Engineering.