There are several products which you can buy which will remove the rust stain. Rust Away is one that I know of. Lime Away will also work. Be very careful with these products however! Dab a little bit onto the fabric with a Q-Tip and wait until the rust stain disappears. Rinse the spot with water as soon as the stain is gone.
Update: So i have been waiting for a sunny day... have tried just lemon juice didnt seem to do much... is out in the sun so will see what magic the sun can do...will read through some of the other suggestions now too
:(Yes, I had the same problem on a large pattern that I got tired of stitching and left the needle in for quite a while. It's been so long, I don't remember if I even finished the thing!:(