When the PDF file is being displayed in Safari, touch the page and a little menu bar will briefly appear at the top. There you'll see a little 'curly arrow' icon. Touch that and it will offer you the option to 'Open in iBooks' and 'Open in...' if you have other apps that can read PDF files. Touch, say 'Open in iBooks' and the iPad will switch into iBooks and, after a wait of a few seconds, you'll see that PDF file there.
Hope that helps, but if there's still a problem don't hesitate to get back to us.
Welcome to the Forum.
Tim
Scotland