As opposed to visiting the webpages of the stories via an RSS feed and saving them to your disk with the Save to disk function in a browser and then using calibre to convert the webpages to something readable on the reader?
But I get your larger point which is that news publishers are running out of funding sources and calibre isn't helping that. To do that I have to say that calibre does not deliberately strip out the ads. The ads are removed as a side effect of making the webpages legible on the reader. If the publishers wised up and included ads in a way that did not make teir websites unusable on the reader, there would be no need to strip the ads.
EDIT: Another purely legal point is tht calibre doesn't actually distribute the repackaged content. It would distribute the content if I set up a website and made the LRF/EPUB/MOBI files avaialble for download
EDIT2: And from a purely practical viewpoint, the way online adds works is by page views. calibre presents itself as the firefox browser, so it should still register as a pageview. In fact because it downloads *all* the articles, not just the ones you actually read, it's good for the publishers