I really think this issue is rather cut and dry. Obviously as a business Dungeon needs to appeal to the broadest possible audience, and that's what generic adventures do. There's also, in some cases an issue of backwards compatibility: Some elements of the WoTC settings (I'll pick on Warforged as an example, even though Eberron is near and dear to my heart, or maybe even the Shadow Weave in FR) are not as readily transferrable into anyone's homebrew. I'm definitely not advocating that the Eberron/FR adventures should strive to also possess incredible 'homebrew friendliness', as I think that resorts in what I consider to be a 'poor' adventure for the genre of that setting. Tensions Rising in 136 is to me an example of this (No offense to Ryan Smalley, who was written several other excellent adventures), which really had no Eberron flavor to it except for airships, a dolgaunt/dolgrims and a House Lyrandar namedrop and well, I can get airships and freaky aberrations in FR, too.
That said, as a fan of both Eberron and FR, I certainly don't mind seeing more content for those settings. However, I feel like that the attitude amongst fans of those settings that lack of adventures set specifically in them make particular issues worthless. It's not as if someone's delivering a magazine with 100 blank pages to you every month your setting isn't present in them. Generic adventures are generic for a reason: They fit well with any setting, FR or Eberron included. Frankly, the excuse that "I buy Dungeon because I don't have time to write my own adventures" doesn't really fly here. Most of the conversions you might have to make (if you even have to make all) are not mechanical, number crunching endeavors, they are story-based, creative ones, which you can probably do in your head as you read through the adventure.
Overall, while I respect the desire for more published campaign setting content in Dungeon, I disapprove of completely devaluing the magazine, which has done nothing but increase in quality in the last several years, over it. Honestly, this debate is become almost Paladin thread-like in its 'Horse beaten so thoroughly it has been reduced to its component atoms'-ness.