I just tested this for about 15 minutes in practice and I don't see it at all.
I made a 6'3", 225-pound HB with 99 speed, acc, and agility and a 5'5", 160-pound HB with the same stats. They look like they're the exact same speed (which, incidentally, doesn't seem that fast). I even ran a 40-yard dash with them on an empty field.
Maybe the smaller guy appears faster because a smaller body is covering just as much space as a big body.
On another note, since EA fixed pursuit angles for NCAA 10, I wish they'd bring back NCAA 09's speed curve.
Speedsters in this game just don't feel that fast.