I was a bit surprised by the column - and I totally disagree that PDF files are only good for printing.
Like you, I only read pdf files on my computer. I've never printed an ebook out - html or pdf. (I even read all of Ken Evoy's stuff on-screen.) PDF is my preferred file format for ebooks.
One thing in the article that really threw me was his comment on PDF having "no navigation bar". No, it doesn't - it has a contents column that, in many ways, is superior to a navigation bar, and the "normal" navigation of just moving from page to page works fine just by scrolling.
I agree with you, though, that the deployment of pdf files needs improvement. It's frustrating to click on a link to download and then get the pdf file starting in your browser. It's also impossible to download a pdf file directly from my email program (Eudora) - it will only open a browser window and start it there. I may start using WinZipSE to create a mini-installer for all my pdf stuff, since it will unzip the files to a specified directory AND open whatever file you designate.
I think we have to take his column in context - he is basically writing about web documents, not ebooks. I think we have created our own use of pdf that kind of bends the normal use of pdf on the web. In that sense, we've created a unique niche that was never really expected by anyone - and we certainly don't fit his "guidelines."