At first I was thinking, wow what kind of a freak has only a 3 inch middle finger, thats so short!.....then I measured mine and its exactly 3 inches :p I have the same problem as you. You kind of get used to it, but its still hard to play certain things. Frets 1-5 are hard to play for me because I really have to angle my wrist in a weird position. Kinda sucks, but I still get by. I advise you to not give up. It gets easier, but don't expect it to be as easy as a person with what I call "guitar fingers" (aka normal/long fingers). It's not impossible though.

Just look at Michael Romeo from Symphony X. He has smaller than average hands and hes amazing.