I assume it is similar to the example I gave earlier. Say we have an zone read to the right the goes for 15 yards. If Jaimes, Hixon, and Cam all get beat they aren't going to get a good grade, while Wilson and Farniok will probably have a positive grade since you assume they helped the runner gain the 15 yards. Therefore, three of our five linemen will have a negative grade on a play that gained 15 yards.
Again, I'm not advocating that PFF is perfect by any means. I do think they bring a perspective that is unlike anything else out there.