For one thing, many leagues award 6 points for a rushing td, but only 4 for passing tds.
The main reason, however, is that the dropoff at RB is much greater than at QB. If you look at the difference between Warner and, for instance, the #2 and #10 QB's, you'll see that (in most scoring systems) it will be less than the gap separating Faulk from the #2/#10 RB. Warner may well score more points than Faulk, but Faulk will put you in a better position to outscore your opponent.
Consider the following model: in a ten-team league where you only start a QB and a RB, Faulk plus the last QB picked will in general outscore Warner plus the last RB.
(See for instance Genghis' post here: http://www.fantasyfootballcafe.com/forums/viewtopic.php?t=202
In this case, Faulk/Stewart beat Warner/Rhodes by a score of 610 to 562.)
Still, Warner at #5 is a very nice pick. If you can get a solid rusher in the second round, you'll be in very good shape.