I traced a long-term plantar fascitis-like foot problem to wearing Clark's Natureveldts (remember those?) around Italy on my honeymoon. The footbed was just like the Desert Boot: flat as a board. Many miles of walking later, my feet were in rough shape.
Cannot tell you why, but the two pair of Desert Boots I wear regularly throughout the year do not bother me at all, particularly with normal daily wearing (work, play, no hiking). YMMV, of course, and naturally other posters have given great advice regarding insoles, but paired with a thick pair of socks in the winter, and even (Heaven forfend! Call the Sartorialist!) sockless in the summer, I'm incredibly fond of my suede deserts and wear them au naturel.
That is, they're au naturel. I'm wearing clothes. Usually.