Well, I do use FT to generate my relief and coastlines. Most of the work I do is in Adobe Illustrator, with some touch-up and raster effects in Adobe Photoshop. From what I've heard, GIMP is a free clone of Photoshop and Inkscape is a free clone of Illustrator, so if you don't want to spend the money you can try those.

I own an older version of Campaign Cartographer, but I think it is brutally difficult to use and I agree that it does not seem to do a particularly good job of making atlas-style maps even if you DO know how to use it.

-Rob