I know what Frank's talking about, but I don't think there's a problem about any group pursuing its interest via a letter or two as much as its one of the demographic oddities of doing comic strip work. Ideally, newspaper editors would read complaints received in context, but a great deal of them have little to no interest in a comics page and prefer a comics page with as little fuss as possible. Unless you hit with a lot of papers really quickly -- like Doonesbury and Boondocks did -- giving your strip the sheen of a national powerhouse, you're in great danger of falling under a "not worth it" designation in many editors' minds.
I don't really see it as a problem or anyone being at fault as much as it's a unique facet of a bizarre and tough marketplace. It's a weird, arbitrary business. I used to think this was funny until it became my vocation, but my teenage brothers and I were the ones who pretty much selected new strips for the newspapers my father edited, Dad stepping in only to veto "Rudy."
I still think any paper should give space to any professional comic strip done by someone in their home area. It's just good business.