As far as I know it’s pretty straightforward. I can’t see any hidden meaning in the four-word phrase, and I don’t know that it can mean anything other than what it says.
What your professor must be referencing is the fact that when the motto has been challenged in court, the courts have upheld the motto by explaining that it’s not violating the Constitution by establishing a certain or specific state religion. In other words, the courts say that “In God We Trust” is just a motto or patriotic quote. It’s not an official government statement sponsoring religion and it’s not saying “In a CHRISTIAN God We Trust” or “In an ISLAMIC God We Trust”. I think that’s where the line would be drawn Constitutionally, and I think that’s probably what your professor is referring to.
In my personal opinion, the fact that it is the official motto of the United States (which it is by an act of Congress and the signature of a President), does violate the Establishment Clause in the First Amendment of the Constitution. If “Congress shall make no law respecting an establishment of religion…”, then I believe Congress should be precluded from officially sanctioning a national motto (which supposedly speaks for all Americans) that not only mentions a religious deity and our belief and trust in it, but even specifies that this God sanctioned by Congress and the President is representative of a monotheistic religion. So, non-believers and polytheists alike are misrepresented by the official motto.