Linus has strange and mysterious stacking powers. Charlie Brown has ordinary and understandable smart aleck perceiving powers.
It's not just that Charlie Brown is bad at making card houses, or that Linus is good at them. It's that the baby character is so much better at it than the older kid. This is kind of a repeat of Schroeder musical genius, and, to a lesser extent, Lucy's ability to beat Charlie Brown at checkers. This stops when Sally is introduced, who appears to have picked up the same gene of mediocrity Charlie Brown got.