Research is typically a profit center for the university. The standard cut (known as "overhead" in the biz) is 30% of research grants. Capital equipment (typically defined as stuff costing more than X dollars) is taxed at a lower rate (usually 10%). Research assistantships are also charged 30%. Also, any modification to lab facilities (electrical or carpentry for example) is usually required to be performed by university staff at a cost (to the grant) of around 2 to 3 times union rates.

In the private university I work for (in research) the University keeps all patent revenue, keeps a portion of all grants, and requires the lab to pay for space- I was really surprised to find out how much went towards that. There's also a lot of really annoying charges, like costing $180 to reactivate ethernet jacks that they deactivate when a device hasn't been plugged into a port for three months.