Okay its mine time to chime in.. The old married guy will help.
There could be a couple possibilities here.
1st - She is worried about losing you as a friend if something where to happen to you since things seem to be moving kinda fast.
2nd - She knows you are great friend material, but isnt sure if you "boyfriend" material. I always managed to be this guy through school. It sucked, but its really not that bad just being friends.. Atleast not until one of you find a different gf/bf and your close friend relationship kinda dies off.
Anyone can work out problems if you both desire to make it work. Its so much easier to give up. The only way to really find out is to sit down and have a nice, long, deep talk about your feeling with eachother and whats going on between the two of you.
Good Luck!