It might be because once one flag starts flying, others are soon to follow. Before you know it, the u.s. flag will be disallowed by policy, not because admin is anti American, but they don’t want problems caused by flags for every cause.
Bullcrap. Every school I ever saw in Texas or Oklahoma had a US, a state and maybe a tribal flag.
Flying the US flag doesn’t mean you are obligated to fly every other flag someone dreams up.