Fr. James Martin explains it all succinctly in The Washington Post:

Here are a few things to bear in mind, so as not to exaggerate his words:
Pope Francis was responding to a question in an in-flight press conference, during the return leg of a papal trip, when reporters usually focus on the neuralgic issues associated with the recently concluded voyage. In other words, the pope didn’t raise the topic himself; nor did he mention Trump’s name in his answer. So the notion that he was going out of his way to “attack” Trump is ridiculous. Rather, the pope was answering a question put to him by a journalist as sincerely as he could. (Also, he assiduously reminded people that he was not telling them who to vote for. He couldn’t have been any clearer about that in his brief answer.)
The pope seemed not to have known exactly what Trump said, and was reluctant to pass judgment on the man. He said explicitly, “If he said things in that way.” Besides, this is the man who asked, “Who am I to judge?”
Like any good Jesuit, who knows that this rule is ingrained in the thinking of Saint Ignatius Loyola, the Jesuit founder, the pope says that he is giving Trump the “benefit of the doubt.” As Saint Ignatius wrote in the “Spiritual Exercises,” “it is necessary to suppose that every good Christian is more ready to put a good interpretation on another’s statement than to condemn it as false.” That is, one should always assume the best possible interpretation of a person’s words and deeds. So the pope’s response was couched in explicit terms of “if he said this” and with an implicit “perhaps I’ve misunderstood him.”
But in many ways, the pope’s words are being interpreted correctly.

Read on to find out why.

What the Pope Did and Didn’t Say on the Plane