Tomlin was trying to have it be a team thing, that whatever they did they all had to do. They couldn’t agree on what that should be so he decided to keep ALL the players off the field, apparently not realizing that this would be just as much a statement as anything else they might have done.
I don’t know what motivated Villanueva to go against that, I doubt he’s a Trump supporter so I don’t think he was trying to be political. I choose to believe he stood and honored the flag because (a) he’s been shot at while wearing it on his shoulder and (b) he’s seen other men die because they were wearing it on theirs. And Sunday was Gold Star Mothers Day.