It's percentage of ballots, as far as I know.
One of the ESPN writers was lamenting the fact he could only vote for 10 guys, and he remarked it was stupid that if a ballot is cast with more than 10 votes, it's scrapped and doesn't count against the % (same as a ballot not submitted)...but some idiot can submit a blank ballot to make a statement, and every player on the list takes a % hit.
In one sense, I agree with this. If you submit a blank ballot to stick it to the PED users or "generation", you're also hurting the little guys who may not even stick around on the ballot if they don't hit the minimum. Those guys probably aren't getting in, ever, but they're still getting unfairly screwed by these "statement" ballots.
I would find it VERY hard to believe that a voter could look at a ballot in any given year and not find at least ONE name he thinks should be in the HOF. If you don't want to vote for Bonds, Clemens, etc., that's fine, but don't use your ballot to make a blanket statement against everyone.