You might want to ask about your issue in the specific Calibre subforum a bit down the forum list.
The papers I get (LA Times, Seattle Times and one or two others), all appear almost like any page in a book, with book-like font sizes on my Kindle3. I have them automatically mailed to it. I don't think I set it up in any special way. I just chose the periodicals I wanted and they sent across very readable. Have you set Calibre up to generate mobi - the format that the kindle uses?
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