Another possibility is that YC could maintain a higher percentage of success, at a lower individual return. Because YC attracts some of the best young talent around, is very selective in funding, and seriously optimizes their fundees chances of success, it's not unreasonable that YC could maintain a better batting average than the VCs.

Another possibility is that because YC tends to form definite relationships with the founders they fund, they can count on the law of large numbers within, not just between, teams. For instance, YC lost money on Kiko, but is also invested in justin.tv--if justin.tv makes it, the YC[kiko folk] relationship could still end in the black.

N.B. This is all complete speculation; any more insight from pg would be appreciated.