How Trump reasons it, per the source:
General Flynn is a good man who served his country admirably.
The Russia story is “fake news” and Flynn did nothing wrong by having the conversations with the Russian ambassador. (Though obviously the President has acknowledged publicly that it wasn’t appropriate for Flynn to either mislead the Vice President or not remember the phone call where they discussed sanctions.)
When Flynn went to Russia in 2015 to deliver a paid speech and take a photo with Putin, he was acting under an Obama security clearance. This is a point the President wants to stress and you can expect to hear the White House press team repeat it.