How the chief executive puts together his cabinet and staff are usually a President leader first test. Right now the controversy over Flyn's resignation is alarming.
We have clear evidence that a foreign nation has deliberately interfered in our elections and clear evidence that Trump administration officials colluded with Russian intelligence prior to taking office. It is highly unlikely given Flyns understanding and respect for chain of command that he would have done so on his own.
So what the American people want to know is "What did the President know and when did he know it?".
This is what Nixon was asked on Watergate, Reagan on Iran/Contra and Clinton on Lewinski.
This a fair question and if Trump has any survival sense he will take a chapter out of Reagans book and proactively cooperate with an independent investigation as this has the potential to become the biggest political scandal in US history with enormous constitutional consequences.