A perfect example of a common navigation problem by xkcd.

Who is your navigation for?

The specific, but diverse populations within a University have  caused some horrible navigation choices. Who's your audience? If a University directs their navigation towards your students, the faculty can't find anything. If they direct it towards the faculty, the students can't find anything. That's not even considering other audiences like parents, sports fans, and potential students.

It's not a problem specific to Universities, they just make a great scapegoat. The same problem can be seen in much simpler sites. The audience the site design was targeted to, and the real audience aren't always the same group of people.

Who was your site designed for? Did you target the right audience? Do you have more than one audience? Are they different enough that it would require compromises be made with aspects of the site like navigation? In the case of Universities, they may even be diverse enough to require different site structure or navigation. State government sites can be the same way. A number of state sites have taken to dividing their home page by audience and giving each audience their own version of the home page. The Delaware state government site is a reasonable example. They use tabs for each primary audience.

It's unlikely that a personal or small business site would need to go to this extreme, but it is very possible that you're not targeting the right audience. Take a moment and pretend to be a member of your primary audience. Look at your site as if you'd never seen it before. Does the organization and navigation make sense? You might like what you see, but you might be surprised too. Good luck.