1. If you buy a home in one of these HOA communities, you have to follow their rules.
2. In fairness to the HOA, if they waived their rule for him, they would have to let everyone fly whatever flags they wanted.
I agree with your statement about HOA’s; I worked for an HOA management company, and you couldn’t PAY me to live in one of those communities. Who want to by a house with the name of the HOA ALSO on your deed?! Insane!!!
The rules are mostly spelled out. Buyer beware.
Your second point is an important one. I’m very familiar with how the law treats these HOAs in some states, and as a matter of course lawyers will typically advise their HOA clients to strictly enforce their rules when it comes to this sort of thing. Otherwise, they may find themselves on the wrong side of a legal battle with someone who wants to fly a Nazi flag, a flag with obscene words or images, etc.