Exactly, the government is extremely large and not all the NSA. Sometimes the left hand doesn't know what all the thousands of right hands are doing and can't possibly care.
Tor has probably saved more than a few CIA agents' lives, not to mention free access to the Internet being a powerful tool for undermining authoritarian regimes.
> Tor has probably saved more than a few CIA agents' lives
Tor's main purpose is to allow agents of US intelligence agencies to communicate back with the home base.
"Giving free access to the Internet being a powerful tool for undermining authoritarian regimes" makes it harder for an adversary to focus solely on intelligence agency agent traffic.
I'm not saying Tor is backdoored or monitored, though it's heavily monitored.
When enjoying the benefits of Tor, it's wise to also remember Tor's main purpose.