I thought the rules only prohibited contemptuous comments about officials or attending political rallies in uniform. I didn’t know they prohibited positive comments about sitting presidents. As has been noted, they certainly didn’t stop the live in the military from rubbing everyone’s noses in BO’s social experiments.
Positive comments about the President aren't what this is about; they were flying political campaign flag, and under existing DOD instructions, they're prohibited. They can, however, fly whatever campaign flags they want on their vehicles (in most cases), and on private property.