I think, in a word, the problem is one of presumption. Gavin Pretor-Pinney starts from the hypothesis that clouds are underappreciated -- fine, it justifies the book/documentary/book fair tour but it's probably best not to go on and on about it because that's the bit which does not add up -- looking up at a particularly startling cloud formation and going WOW! is a human commonplace, and most people, asked about clouds -- they'd have a thing or two to say. Not all negative.
His Cloud Appreciation Society (and the documentary, and doubtless the book) quote a poem by Shelley, author of that aesthetic snobbery that assumes in the author a wildly charged emotional connection with a thing that the common herd could not possibly understand. This irritates me. He irritated me. Which is not that you shouldn't see the documentary, you should, it's quite good, and I'll doubtless get to his book (though the lack of illustrations is a barrier -- I remember the cloud formations pictures in the Ladybird Book of The Weather most vividly).
Also, about halfway through, I became frustrated by the photography, and turned on Flickr to pick up some clouds which were a bit more like the ones I remember from when I was young*. There wasn't a shortage of photos, and most of them were awesome (though the one of a huge spaniel running through a sunset with stars twinkling out of its feet may have been, hm, shopped) bearing out my supposition that, far from being a rare thing, love of clouds is such a commonplace that most people would not bother to mention it unless they were drunk or otherwise in a state of emotionally charged blither.
Ooh, just a side note. Does anyone else remember an experiment where you filled a gas chamber with steam and turned it into snow with a carbon dioxide fire extinguisher? Or am I just imagining that? In one of the prettiest sequences in the documentary, he turns fog into snow this way -- but misses it, as they couldn't afford a cameraman that night, so it's just him and a camera on a stick. As he discharges the fire extinguisher, there's a dintinctive flurry of snow, but by the time he's emerged from the mist, it's blown away, and all that are left are tiny, sparkling ice crystals, which he can't decide about. Do they represent a success or a failure?
Success, Gavin, but it wasn't that hard a sell. People like clouds anyway.
*Vast, hallucinatory cloud landscape sunsets splattered across autumn skies which looked like a distant view of another world.