Much in the same way that art majors aren't expected to practice mathematics at a high level, football players are recruited to the university for a different skill set. It's not as if admissions simply looks the other way when considering the applications of football players. Perhaps this would be an issue a millennium ago, but the realistic purpose of universities today is to ensure that they educate individuals who will have an opportunity to impact the world positively, with the hope that this improves the university's reputation down the line. Football players have a much greater chance to do so compared to the average student, so why shouldn't the university admit them on a different basis?
In addition, this entirely ignores the mental skills necessary to play dominant football at a high level. It's not as if elite safeties, for instance, are simply standing there and waiting for the guy with the ball to run toward them. The extent to which football is a mental game means that these guys, at the very least, must have a high-level understanding of the game to be successful.