Because he knew the corrupt Comey McCabe FBI would leak it to the corrupt media which would use it to derail Trump before he even took office. Think back, there were efforts to try to stop the inauguration and it was all about “Russia collusion”.
In deciding to lie, Flynn essentially fell on a grenade to protect a buddy.
Flynn was director of DIA
He had clearance above this agents, who could write notes of what he said/unless-said notes were from the Clowns In America