I haven't read the article in Vogue, but I don't think Emma Watson is being at all unreasonable.
I agree that she is probably facing a very difficult time in her life right now. Going to college is not an easy transition for your average young person, and when you add in the fact that she's been filming Harry Potter movies since she was, what, 11? and hasn't attended a regular school in years, you don't even need her celebrity to explain why she's finding it more difficult than most.
On top of that, a whole lot of celebrities attempt to live normal lives outside of their work by trying to draw a clear line between their personal time and their public time. They'll still get photographed, and they'll still get noticed, and they can't ever truly turn themselves off outside of their own homes, and I'm sure they all realize that. The reasonable ones don't pitch fits about it, either.
The thing that's hardest for Emma Watson, I think, is that she doesn't even really have a home she can retreat into, not if the other students at her university don't allow her to do it. For now, that campus is the closest thing she's got to home (especially since it sounds like she's living in a dorm). I don't think it's at all unfair to hope (and to ask) that her classmates try not to treat it like she's on the red carpet.
It doesn't really sound like she's made any demands, at least based on those two quotes from the link. She didn't ask anyone not to post pictures of her (although I'd hope that people would refrain from taking pictures of her when she's in a towel!), she just expressed her surprise (and perhaps appreciation) that people have refrained from doing it. And she didn't tell people she wasn't going to sign autographs, she asked if it was okay not to. It does seem like she understands the paradox of her situation, as DigitalPumpkin said, and she just hasn't completely figured out what to do about it. Hopefully, she'll have the opportunity to learn.