While I agree that the iPad's file management scheme needs improvement, it's pretty easy to download, organize, and read PDF files using PDFReader Pro (available in the App Store). You can find a document using Safari, and paste the URL into PDFReader Pro to download and save it in the app.
For documents stored on your computer, Dropbox lets you open PDF files in either PDFReader Pro or iBooks. This is probably as close to "syncing" as you can get right now.
If you use iDisk, you can install the iDisk app, e-mail yourself the links to PDF files stored on your iDisk, and then open them up and save them as described above. Klunky, but it works.