PDFs are great when you want to save a document for later, offline use. Like a product manual, which one may refer to once in a while. You can refer to your local copy, and not have to download it every time.
PDF's are also great for preserving the formatting on documents. It takes a lot of effort to get the formatting to appear exactly the way you want it to in HTML in every browser. Now imagine you have 5,000 separate product manuals, which one can either simply and easily export to PDF, or have the headache of converting to HTML (and losing portions of the formatting in the process), and it's an easy choice.
Using PDF's for major portions of websites is stupid, but they do have their place. It's all a matter of using the right tool for the job (or at least the least bad tool).