They are going to pay for all the facilities that are available for students. Due to the high costs of science courses, many universities say that £9000 is not enough, and the Russell Group at least are lobbying for this to be raised. Here are just some of the things that universities have to spend money on, which students often don't think about.
-Library facilities, books and staff.- subscriptions to journals can be very expensive.
-Computing facitilities and IT support.- often universities provide computer programs free of charge to their students, but they have to pay for the liscenses for these. They also have to maintain and update their on site computers, printers etc. Most universities will have litterally 100s of computers on site.
-Utilities- especially electricity and water.- Think about how much electricity one building in your university must use. The lights are on constantly, there will be computers running all day. In winter they have to heat these large buildings.
-Admin staff, such as those that work in your school/faculty office, as well as all the things they need to do their jobs, like stationery, phone lines etc.
-Specialist support staff- technicians, finance advisors, disability assistance etc. Don't forget, most of these staff don't have the long university holidays off. They are paid all year round. You might not notice them much, but you would probably miss them if they were gone, and complain if these services are not provided.
-Other staff- such as cleaners.
-Maintenance of buildings and grounds. This can be quite expensive. However, they are important to universities, as poorly maintained buildings are likely to put off prospective students.
-New building projects- as universities have expanded in size, they may need extra buildings to use as halls or for teaching. Whilst they will usually try and get grants/investors to pay for much of these, some of the money may come from their usual budgets.
-Specialist equiptment- ranging from reagents for experiments to lab equiptment to other specialist equiptment that might be used by people doing degrees like engineering. Sometimes, things will get broken and need to be replaced or new, improved versions will be available that the university wants to buy. Some things, like chemicals, will need to be constantly replaced as they are used up.
Basically, universities have to now cover the majority of their running costs from student fees. Whilst not ever single thing they supply directly benefits every student, most students will use at least some facilities. Some courses, especially science courses, are much more expensive to run than others, so these courses are subsidised by the other courses which are cheaper to run.
I think a lot of universities are running on less money than they had before. The accademic staff are certainly under more pressure. Due to the way research funding has changed, staff are under even more pressure to regularly produce research. As well as this, they are under more pressure from students to give them more support/time for their money. Many accademic staff also have additional roles, like advising government comitees, or being expert witnesses at trials, which they have to fit around their main commitments. However, if they stopped fufilling these roles, the country as a whole would suffer.