I don't think airports have the authority to make zoning regs - that is a city plannng commission's responsibility. If the taller flag pole constitutes an airspace obstruction, then it is a safety issue, and the flag pole has to be lowered.
I've seen the large flag and it's impressive. The 132 ft. pole is not going to be a safety factor for any airplane coming in or out of Eau Claire or Chippewa Falls.