I think there's a litany of reasons why our endowment numbers are behind Stanfurd and even U$C.
1) We do a terrible job of grooming future donors. When I was at Cal, I didn't feel like the administration and support staff cared about the success of their students. A large chunk of that might come from being at a school with so many students, but from my experience having worked on-campus, it felt like a large chunk of the employees (not all, mind you, as there are excellent ones too) are just going through the motions and looking at a cushy pension, not because they actually care about the students.
2) Since in-state students cannot be charged tuition (that's why they're called student fees), it feels like the school nickle and dimes you when you look at the breakdown of what you're paying for. At Furd and U$C, you get everything neatly encapsulated (or hidden) in the tuition, so it feels like they're giving you a bunch of free perks (i.e. you can get a new ID card ever semester for free at U$C, whereas Cal charges you something like $30 for each new card). There's also random fees like the compulsory class-pass fee that's exposed in the breakdown, whereas it's basically built into the tuition elsewhere.
3) The media coverage of protests on campus has painted students as self-entitled brats. For instance, the trashing of University House, setting fires on Sproul, pulling fire alarms during exams, preventing students from going to class, etc. makes it less likely that alumni will be willing to donate, IMO. Even though I know that the majority of students are sane, the vocal minority still bug the hell out of me.
4) Back to point 1, the calls asking for donations just rub me the wrong way. For instance, I graduated with a degree in CS from L&S, not COE. I never got any benefits from COE that COE students got. However, lo and behold after I graduate, COE comes after me with phone calls and letters asking me to donate to them. Many of my friends who also graduated L&S CS have gotten the same calls and share a similar sentiment. Ironically, I have never gotten any calls or emails from L&S asking me for donations...
5) Of course, the elephant in the room is that Stanfurd students may end up becoming more financially successful than Cal students on average. Now, that could be because they tend to come from wealthier families to begin with, but regardless of the reason it does appear that Stanfurd alums tend to have more disposable income, or at least more heavy hitters who can toss around hundreds of millions in donations at a time.
6) There's a feeling that the school tends to waste your money, given how much bureaucracy and red tape there is. For instance, when buildings go up on campus, they take in extremely long time to get put up. I don't know about Stanfurd, but at U$C the buildings are completed much much quicker. It could be that it legitimately takes longer to do construction at Berkeley, but the overall feel is still that we are more wasteful with the money they have, since you have to pay a retention fee for the construction company even if they can't work on the site.
7) Having worked on-campus, I may be biased, but there's a huge use-it-or-lose-it mentality when it comes to spending. Often times, departments or organizations would spend money on things they don't need rather than have it be reabsorbed into the University's general fund. From an organizational perspective, there really wasn't a whole lot of community between different departments; everything was pretty much it's own isolated little business unit with very little cross-departmental interaction or communication. I don't know if the same issue plagues Stanfurd, but this is something that really bums me out, especially when we're already in a budget crunch.
8) Operational Excellence was a joke. While I understand it's an investment, spending $3 million during a budget crunch doesn't send the best message to students and alums. A good friend of mine worked on the project at Bain and would constantly joke about how ridiculously easy it was to find areas to cut costs and consolidate resources. He mentioned that the school could have probably turned the project into something Haas could work on instead of paying Bain $3 million.
All that being said, I still donate, but the above are reasons why I can see others may not be so willing.
Edited to add:
I just remember another thing. Getting into the necessary classes (forget classes I wanted to take) was a huge PITA for me, either because classes would be full, or they just wouldn't fit in my schedule because there would be only one 400 student lecture rather than four 100 student lectures. Sadly, this kind of stuff is undoubtedly due to funding, and the problem just snowballs, as more students become jaded by not being able to take the classes they want or need and wind up leaving Cal with a soured relationship.