i have the same problem with my dog - i have been making sure every day that i am rubbing her paws and getting her used to having her feet touched. i'll make sure i'm really happy and upbeat when i'm doing it and lots of praise.
the next step is actually taking out the clippers and touching them to her paws but no clipping yet. i'll just gently touch her paws with the clippers and say in a really cheery voice "good girl! goooood girl... " and then say "clip clip clip!" if this is going well you can actually pretend to clip the dogs nails. this gets her used to the clippers and calm down a little. my dog is reeeeally nervous about nail clipping, so i only do one at at time. ie, monday i will do one, tuesday i will do another, etc etc. if she acts up or starts to freak out, i just do the paw rubbing and pretend clipping, and that's it for that day. i have also heard another thing to try is to put a towel over the dog's head so they can't see what you're doing - this calms down some dogs although it hasn't really worked for me. hope this helps.