At least that's the "official" version; the more underground explanation is it was a bone tossed to drivers amid a rumored mass park-out in the 500 to protest NASCAR's roof blade aero package; said parkout never happened.
But the question remains - is it really wise to have a yellow-line rule?
Tony Stewart passes several cars below the yellow line at the start of the final lap
After getting drafted back to about 13th in the 1996 Daytona 500 we see Dale Earnhardt passing in what would be today declared below the yellow line
When Earnhardt and Ernie Irvan battle side by side for the lead Terry Labonte blows past them both by diving below what today is the yellow line
The wild finish to the 1999 Daytona 500 saw plenty of passing below what is today the yellow line
Then there is the most famous example - Junior passing on the apron of Turn Three in 2003
As seen in these examples and also by such dubious yellow-line penalties as Tony Stewart in 2001 (Firecracker 400) and Regan Smith in the 2008 Diehard 500, one has to dispute the sagacity of having a yellow line rule - one is hard pressed to see where it serves any purpose.