While we still don't know if Trump actively colluded with Russia, we do know that Trump screwed up and put the safety and security of our nation in jeopardy. He was warned about Flynn by Obama days after the election and did nothing and later by Yates and still did nothing for weeks until the whole scandal became public. 
Trump also lied. He knew of Flynn's contacts with Russia but then went on for months telling us "neither he or anyone in his administration had anything to do with Russia." There is no explaining that away.  
To put Flynn in charge of National Security with the knowledge of his Russian ties is either a deliberate treasonous act or complete gross incompetence - neither of which can be tolerated.