What's wrong with honering the president?
Nothing, but doing so while in uniform (and especially from a DoD vehicle) is very much against the law. As it should be.
Well obviously this shouldn't be allowed, but it isn't that big of a deal.
Actually, it's a big deal. The military of the United States cannot be political or demonstrate any preference/allegiance/support for a cause for any particular entity or organization besides the United States of America.
Yes, but this sounds like it was probably some individual soldiers who were showing support for Trump without thinking about the implications. It would be different if it was the whole convoy or if Trump or a high ranking officer or official ordered it or something.
It was the LEAD vehicle, everybody in the column knew they were flying that flag, including whatever Major (or whatever officer was in charge, I don't know what level of officer would be in charge of a convoy) was in charge. THAT person is in the most trouble (or at least better be) because that person really really screwed the pooch here.