Ok but for the Raytheon thing, they werent making merch of it, they were just flying it as a flag, so the creator couldnt have stopped that even if they wanted to because they dont have copyright over waving a flag.

This is just not how copyright works. Flags aren't magically exempt if you put them on a flag poll. The progress flag is a creative work being publicly displayed by a for-profit institution for it's original purpose without transformation/commentary/criticism and there is a viable copyright-free alternative; this doesn't fit into any fair use exceptions.

The creator maintains 100% legal control over the these commercial uses.

The creator says that any money made by getting corporations to pay is used for lgbt funds and charities

The creator says 25% of sales from the online store go to charities. However, the online store is explicitly only for noncommercial use. Commercial use is sold through private deals, and as far as I can find the artist has never stated that these were anything but for personal profit.