Recouping Support Cost (Software Licensing & IT Services)

We currently charge our users a flat fee to cover support services and software licensing. Within this fee, we cover licensing fees for MS Office and other Microsoft products, our network applications, enterprise-wide applications, and development work to support the enterprise applications (such as custom reports, etc.)

How do you recover these costs? Do you do the same for your departments/users? Or do you just suck it up as part of IT departmental overhead?