Seems like these covenants are in volation of the 1st Ammendment. Maybe the ACLU should give this vet a hand.
T_O_B
No - the Amendments pertain to governmental actions, and that's not the case here. It's a contract; the owner signed the contract when he purchased the home. Legally, he agreed to the restrictions.
Now, that doesn't mean that the association can't create an exception - it can. They should do that, while at the same time applying reasonable restrictions - size of the pole, or size of the banners or flags flown. I'm sure the idea behind that covenant was to try and keep the appearance of the neigborhood "clean"; they can accomplish that while still allowing the guy to fly his flag.