When they feel compelled to do something like this, their first admitted entry into a presidential race, it only flames support for him. The media continues to miss the primary dynamic of this election, as evidenced by Bernie's run, which is a complete rejection of the establishment and status quo. And by doing this the USA Today actually improves Trump's chances of winning.
http://www.usatoday.com/story/opinion/2016/09/29/dont-vote-for-donald-trump-editorial-board-editorials-debates/91295020/