Over the years, I've become convinced that there are lies, damned lies, and cost accounting. What I mean by this is that "true costs" for various items in a business or at a university (a type of nonprofit business, after all) are sometimes allocated in whatever way is necessary to bolster a particular argument at hand. If those making an argument want something to look like a bargain, no problem, there's a way to do the accounting for that. If those making an argument want to make something look so expensive that it's economically unattractive, no problem, there's a way to do that, too. I remember as a postdoc when the part of Lucent Technologies that dealt with real estate argued (apparently successfully) that they should get rid of the simple general stockroom because somehow having the square footage allocated to that use was losing money. So they shut down the stockroom, and had a couple of hundred PhD scientists and engineers spending their (expensive) time ordering 4-40 screws from McMaster Carr online or over the phone instead of just walking upstairs and grabbing some.
Let's take an electron microscope as a test case. Suppose a university or company buys an SEM for $350,000 (for the sake of round numbers). How much should they charge, fairly, for its use? Let's assume that this is a shared tool and not just sitting in one person's lab. This microscope and associated hardware take up something like 100 ft2 of floor space. The microscope also needs electricity (say 1 kW) and cooling water. Now, a university is unlikely to charge a department or faculty member "rent" on the floorspace, but a large company may decide to "tax" a business unit for space at some rate. The electricity and cooling water are likely part of a university's or business's "overhead". Overhead charges are assessed when it's difficult to trace a particular designated responsible source for certain kinds of costs-of-doing-business. For example, the overhead rate at my institution is 52.5%. That means that for every $1 of direct research cost (say a grad student's salary), the university charges my research account (and therefore the funding agency) $1.525. That "extra" $0.525 goes to cover the university's costs in, e.g., keeping the lights on in my lab, the air handlers running for my fume hoods, and the road paved outside my building.
If the university or business wants to maintain the electron microscope, they probably want to buy an annual service contract for, say, $25K. Now, in the absence of a staff person to run the system, you might think that a reasonable user fee would then be $25K divided by the number of hours the system is used (say 2000 hours per year). Not so fast - you have to charge overhead. Moreover, the university or business may decide to depreciate the SEM. That means that they may have an interest in replacing the SEM eventually, so they are allowed to tack on a depreciation cost, too. For our example, a typical depreciation schedule would be seven years, so in addition to the actual maintenance cost, they would tack on, in this case, $50K per year. There are major federal rules about depreciation. For example, you can't buy something with a federal grant (e.g., a NSF "Instrumentation for Materials Research" grant) and then also depreciate it - that would be like double-billing the government, and that's not allowed.
If the university or business does have some fraction of a staff person responsible for the instrument, it may be fair (depending on the discussion) to consider a fraction of that person's salary (plus fringe benefits [e.g. health insurance] plus overhead) as a cost to be recovered as well.
So, the next time you are paying $30/hour for access to an electron microscope, and you're wondering where on earth that figure came from, now you have at least some idea. You can also see how administrations can sometimes argue that they "lose money" on research - they cannot always recover the costs that they put into things (e.g., the actual overhead income may not cover the utility costs), and sometimes they choose not to (e.g., by not charging rent for space). This is all stuff about which I was blissfully ignorant back in my student days.