No, two separate things. Those who were forced to do the cover-up were innocent of the initial 9/11 attacks on the WTC at least.
Why would the U.S. government protect the perpetrators? The answer is: out of national security. The Bush administration could simply not suddenly say that no planes were involved in the 9/11 attacks when almost everybody already had seen the planes crashing into the WTC towers on television. Today Barack Obama may be able to say that no planes were involved, since people are no longer as traumatized as they were when the attacks happened back in 2001.
None of that makes any sense.
... And they wonder why people laugh at them...