I don't see anything wrong, since stories does it all the time, and as others have said, it can imply a certain feel to your character/setting. (Ivies/Oxbridge=elitism, technology products=what OS type you prefer, etc).
My MS (NA dystopia) uses my alma mater a lot (indirectly) and The Odyssey as a referential point, and it's supposed to show a certain storyline/mystery for the reader. It's also an inside joke for myself and for my friends who graduated from said uni. And I use it compared to other places because I know it in and out, and no one can point out that I might be "wrong" or be upset that I'm portraying the place incorrectly.
So research, obviously, is my two cents. If you're using a certain school/trademarked name, make sure you know the ins and outs before using it. Otherwise just create a fictitious brand.
Oh, and to add to the trademark problem, I think the microwave company that was used in American Hustle (the scene w/ JLaw), I think they're suing the movie producers for defamatory remarks. Maybe they've settled, but as someone already mentioned, it does happen.