The Federal obstruction law specifically requires an element of corruption, say a bribe offering to drop the investigation.
Also several legal scholars have now jumped on the part of the testimony Comey spoke about saying the president has every right to end or begin any investigation as the chief executive.
As President Trump can indeed establish prosecutorial and investigative priorities. In fact, Trump could gut the FBI tomorrow and put the DOJ back in charge of all Federal investigations if he really wanted to, there is nothing in the Constitution protecting the independence of the FBI as a fourth branch of Government. It all falls under the executive.
So in fact, even if Trump did order Comey to stop going after Flynn, it would not be obstruction of Justice. Sure it would look very bad, bad politics, but not illegal.