I've had the same issue. I need supports tuned on for the outer structure of a piece, but then it fills in my screw holes too where supports are really not needed. I'm actually running slic3r 1.1.1 experimental and it does the same thing.
So far as I can tell there is no way to get it to differentiate. We should all email slic3r support/ feedback and respectfully mention to them that this does not work well. They seem to update the software fairly regularly so hopefully it gets worked out but I think we are just SOL until then.
Edit: this is in addition to the other issue with slic3r 1.1.1 supports- they are too close (touching) the adjacent vertical walls in many cases. This thread on github forums shows a lot of people not happy with this: https://github.com/alexrj/Slic3r/issues/1539
Basically, slic3r 0.9 was the last good version for supports. 1.0 and up has pillar supports that are nice but still very buggy. Keep waiting for these to get fixed and consider staying with 0.9 for now. I am rolling back to 0.9.
UPDATE: Slic3r 1.1.2 is out now (5/9/14) and they have fixed both issues! It no longer generates supports through your screw holes and the pillar supports are no longer touching the adjacent vertical surfaces!
SD4 w/ RUMBA, E3D Volcano, all bearings, glass bed