The cost center vs. profit center concept has some utility for accounting, but overall it makes more sense to model the business as a modular system seeking a global optimum, a la Goldratt, rather than a set of separate sub-organizations each to be optimized separately.

In other words the business as a whole should be viewed as a singular profit center, and each department or project should be evaluated in terms of how much it contributes to optimizing the overall performance.