Because if it had been addressed properly when it happened, there would have been a shit storm. They tried to keep it under wraps for as long as they could, to protect the program and Joe's legacy, and it became, rightfully, an even bigger shitstorm.
He knew exactly what was being described to him, btw. The rhythmic slapping sounds as described by Mike McQueary himself. Pretty easy to figure out.
What I can't understand is how you couldn't understand that this man would certainly allow it to go on. Afterall, this is the guy who "punished" his players for assaulting members of their own student body (hospitalizing some in the process) by having them clean the stadium. No suspensions.
He was and will always be a giant fraud and POS in my eyes.