Used affectionally hombre is a great word and could have endeared him to the people. But he was using it to sort of covertly refer to hispanics, and based on his previous statements, Mexicans in particular. What is most damning about this is that he was signaling them out for something they are not doing.
Trump was using the Spanish word 'hombre' to emphasise the difference between Latinos and the rest of the population. Essentially, he was othering them - putting them into a different category than the rest of the public by use of the word. He also said the word derisively, as though he considers Hispanic people and their language to be inferior to English and, by extension, white English-speaking Americans.
Yes, Trump's "hombre" comment was racist because he used the term as an insult. He took a Spanish word and twisted it to fit his view of Mexicans. He will go down as one of the most racist people to ever run for president in the modern era. He should apologize.
You may as well say it is racist to say that something is missing a certain je-ne-sais-quoi. Or that it is racist to use basically any other language in discourse, even if it is used colloquially.
You can argue that you feel that Trump is racist, and that his use of terms like this has derogatory intent if you want, but using the term hombre is just language adoption, which happens in all languages. I have heard french people use english terms for various things, particularly in tech fields - le e-mail, for instance. Is this racist?
Hombre means a man of a particular type when used in English, and just means man in Spanish. Trump saying there are bad hombre here is saying that there are bad men in the United States. When used towards Hispanics, it is not racist to use a Spanish word for man and the word bad when referring to criminals.