The real issue, as Flynn has talked about publicly since he left the DIA in 2014, is the evidence of a U.S. role under Barack Obama and his CIA director John Brennan in facilitating an increase of radical Islam in the Middle East. He has cited the evidence contained in a DIA document, declassified and publicly released by Judicial Watch.
And while speculation was rife that just like the CIA-funded al-Qaeda had been used as a facade by the US to achieve its own geopolitical and national interests over the past two decades, so ISIS was nothing more than al-Qaeda 2.0, there was no actual evidence of just this.
That all changed when a declassified secret US government document obtained by the public interest law firm, Judicial Watch, showed that Western governments deliberately allied with al-Qaeda and other Islamist extremist groups to topple Syrian dictator Bashir al-Assad.
According to investigative reporter Nafeez Ahmed in Medium, the “leaked document reveals that in coordination with the Gulf states and Turkey, the West intentionally sponsored violent Islamist groups to destabilize Assad, despite anticipating that doing so could (and did) lead to the emergence of an ‘Islamic State’ in Iraq and Syria (ISIS).
http://www.aim.org/aim-column/why-the-cia-wants-to-destroy-flynn/
http://www.thelastamericanvagabond.com/top-news/secret-pentagon-report-reveals-us-created-isis-tool-overthrow-syrias-president-assad/
In short, Flynn knew the Obama administration was supporting ISIS. He called them out for it, and they took revenge by setting him up.