Flynn was”fired” by the White House for lying to Pence. Flynn’s legal problems are for lying to the FBI, a very serious charge. Why wouldn’t the FBI charge him? Unless Comey is also comprised by Russia there has to be a reason, cutting a deal makes sense.
When a lower level player is accused of a crime but they have information that will shed light on a larger criminal act sometimes a deal is offered. The “snitch” gets a lesser punishment or immunity from prosecution. They then help the FBI take down the larger criminal enterprise in exchange for their freedom.
Has Flynn made such a deal? It’s possible. Is he willing to take the fall for Trump? Maybe not. If Flynn were to implicate the Trump administration he may have more to worry about than the anger of the President. He may need to be concerned with retribution from Russia.
These questions will be answered in due time. If Flynn is not charged and damaging information is released about Trump, we will know the source.