I have some words of encouragement. My mom and I adopted one of her dogs from a shelter a few years ago (I still lived back home, then.) She was the most timid, fearful thing; she was afraid to even get into our car, and I had to physically lift her in, and even being her up the stairs! She literally had been slinking back in the kennel, to the point that you could hardly notice her; this is that drew my mom to her, actually. We both figured that she would not be as adoptable as the tail-waggers in the other cages.
We gave her her "den" which was a crate with a nice pillow in it. Granted, my mom had her other dog, who was outgoing. But in the months following us getting the new dog, she opened up to people and long story short, she is almost too friendly and will attack a person with kisses!
My point is, there's hope. I would personally be more upset if she exhibited aggressive tendencies. I think that it seems a tad bit harsh for them to reject her because she is timid.