It's better when you work for a university run non profit. Man...non profits that do research, they have it made....
As a graduate student, I feel that a significant portion of the tuition that undergraduates pay goes to subsidize my PhD. Yes, most of my funding comes from research grants, but the facilities come from the endowment (which would otherwise go to funding undergraduate education), and the faculty are largely paid for by the school.
The last one sounds fine, except that the faculty are hardly (if ever) evaluated on their teaching ability. I've been told by multiple faculty that they've been discouraged from spending as much time on their teaching, and that they need to turn out more papers. Furthermore, the university will pay certain "superstar" faculty members far more than others, to make sure they don't go elsewhere. None of these superstars are paid extra because they're good teachers; it's always because they're the best researcher.
This is all great for my career, as it means that I get paid to get my PhD, but it makes no sense from the perspective of the undergrad, the majority of whom won't use the research the facilities, and probably wouldn't be able to tell the difference between high-end and second-tier research when they do.
I think as the costs of an undergraduate education continue to escalate, you're going to see a separation in funding in the big schools between the undergraduate and graduate institutions, and they'll become separate entities.