In the early days of the presidency the White House counsel warned Donald Trump that Michael Flynn had probably lied to the FBI and yet Trump did not fire him until after a Washington Post article.

Don McGhan, White House legal counsel.

Courtesy of Foreign Policy: 

The White House turned over records this fall to special counsel Robert Mueller revealing that in the very first days of the Trump presidency, Don McGahn researched federal law dealing both with lying to federal investigators and with violations of the Logan Act, a centuries-old federal law that prohibits private citizens from negotiating with foreign governments, according to three people with direct knowledge of the confidential government documents. 

The records reflected concerns that McGahn, the White House counsel, had that Michael Flynn, then the president’s national security advisor, had possibly violated either one or both laws at the time, according to two of the sources. 

The disclosure that these records exist and that they are in the possession of the special counsel could bolster any potential obstruction of justice case against President Donald Trump. The records that McGahn turned over to the special counsel, portions of which were read to this reporter, indicate he researched both statutes and warned Trump about Flynn’s possible violations. 

McGahn conducted the analysis shortly after learning that Flynn, on Dec. 29, 2016 — while Barack Obama was still president — had counseled the Russian ambassador to the United States at the time, Sergey Kislyak, not to retaliate against U.S. economic sanctions imposed against Russia by the outgoing administration. 

McGahn believed that Flynn, and possibly anyone who authorized or approved of such contacts, would be in potential violation of the Logan Act, according to two of the sources, both of whom work in the administration.

I would contend that the "anyone who authorized or approved of such contacts" means Donald Trump.  Either directly or indirectly.

It is very clear that Trump, at least in the beginning of this presidency, was very hands on and was involved in essentially all of the decision making.

And that would explain this next part: 

Despite McGahn’s concerns that Flynn violated one or both of these laws, Trump allowed Flynn to continue in his job and only fired him after the Washington Post reported that Flynn had lied to Vice President Mike Pence and other senior administration officials about his contacts with Kislyak. That was 18 days after then-Acting Attorney General Sally Yates informed McGahn of her own concerns about Flynn’s covert diplomacy with Russia prior to Trump taking office.

Why would Trump suddenly fire Flynn if Flynn was simply following his own orders?

I never believed that Trump fired Flynn for lying to Mike Pence, and have always seen that as a convenient excuse.

Flynn was let go because Flynn got caught, and now that he has made a plea deal with the Special Counsel Robert Mueller know EVERYTHING.

No wonder the White House and the Republicans are trying to undermine this investigation.