Apple doesn't allow files used by one iWhatever program (e.g. Safari) to be seen by another program (e.g. Goodreader) directly, every program runs in its own "sandbox" by design. You have to follow the specific instructions for Goodreader to get it to see files. Can you see it in Shared Files under Apps, in iTunes on your computer? (I dunno, I only have an iPod Touch which doesn't support that yet.)
It's either that or use Goodreader's built-in "web server" to upload the files. Hit the Connect button (bottom left I think), then open the browser on your computer to the address displayed on the iPad screen. There will be a list of the files on there, and an upload form.