An investigation is supposed to find evidence of guilt, not proof of innocence.
Clearly, whoever wrote that article is a political hack, or did not spend the ten minutes necessary to listen to Bob Mueller's press conference.
Mueller explained, that from the very beginning of the investigation him and his team came to the conclusion that it is impossible to indict a sitting US president, because under long-standing DoJ policy this would be considered unconstitutional. Therefore, questions regarding the president's innocence/guilt cannot be handled within the confines of the criminal justice system. Basta! Presumptions of innocence or guilt are thrown out the window here, and do not matter, and that headline therefore is bullshit. There is only one institution outside of the criminal justice system that can tackle these types of issues, and that is the Congress.
At the same time, Mueller did offer that the option of declaring the president innocent WAS on the table (at least as a courtesy they could provide, to clear the president's good name). However, Mueller and his team WERE NOT able to provide that assurance. That's it. If someone in Congress wants to pick this up and run with it they can(Dem House leadership does not want to start impeachment proceedings, but more extreme rank and file members do). This would be ill-advised however, and would do great damage to the country.
Mueller is not a "legal idiot". He has run the Federal Bureau of Investigation for longer than anyone, save J. Edgar Hoover, under both Republican and Democratic administrations. He was appointed to this investigation (his appointment pleasing both sides of the aisle), and did not volunteer for it. He was appointed because of his reputation as a consummate professional and patriot who has shed his blood for the country.
He kept silent for the entire duration of the investigation and for a month after its conclusion. His press conference lasted 10 minutes and he took no questions. He has refused to come to Congress to testify, saying he cannot say anything beyond that which is already written in his report. This is not the behavior of a political operative producing "tailored" legal conclusions (for that go to Comey).