Football and the Confederacy

Football was born when players at Harvard, Princeton, Yale,
Columbia and Rutgers, after some experience in playing McGill
undergraduates at rugby, decided to devise something wholly
new for Americans. The first game was played November 6, 1869,
when Rutgers defeated Princeton a glorious event which was not
to be repeated for some years. The two teams played each other
annually, but not until 1938 did Rutgers win again.
The first cheering at a college event also dates back to that
same time (November 13, 1869, to be precise). On that day,
Princeton and Rutgers had a return match, which Princeton won.
In its origins, Princeton was very much a college of the South.
Cavalier families sent their sons there, and the college proudly
turned up its nose at the cod- fish aristocracy of Harvard. So
when the Princeton team utilized the Confederate yell, well known
to those young men as the "scarer" which the rebels had used in
charging the Union forces only a few years before, a new-old form
of verbal encouragement became a collegiate tradition for the
players. (Actually, the Princeton team had used the rebel yell the
first game, but cool heads observed that it winded the players so
much they lost the game. So, in game number two, the same cool heads
lined up shouters on the sidelines to do the yelling while the
players silently stayed with their game. Cheerleaders, take note.)  

Source: The Saturday Evening Post, Nov./Dec. 2006 issue; page 50