Because everyone would just draft QB/WR combos from the same team. (Ie. Tom Brady and Randy Moss). Then, every touchdown thrown, that team would get 12 points! That would be nuts and completely over-inflate a QB's value.
Not sure I buy that. My math is a little shaky, but I think 10 points for a TD is still better than 6, right, so by your logic everyone would do the same thing anyway....
A TD is a TD. Just because Quarterbacks get more TD's than other people doesn't mean they would be inherently worth more - the fact remains that you can get a decent quarterback much later in the draft than you can a decent RB. The other problem with this is that it artificially deflates the value of a QB - not only compared to other positions, but compared to other quarterbacks.
If I want to draft Manning, Brady or Rivers early because they're way better than JaMarcus Russell, why shouldn't I be entitled to getting an extra six points each for the 1.5 more TD's per game they're going to throw? You get an extra six points for each of the TD's that Adrian Peterson scores more than some other RB, right?
Anyway, rant over. It's not a thing particular to this league, obviously, just a general irritation with FF, and one of the reasons I always create a couple of my own custom leagues, so I can set my own scoring. Yahoo! was ok until they changed passing TDs to 4 points a couple years back...