With the release of Apple's iTunes 9.2 and the iBook 1.1 application release for the iPad (this also works reportedly on any iPhone or iPod Touch with iBook 1.1), you can now get PDF files automatically downloaded into the iBook application.

Here is how I was able to get it done:

1. Subscribe to a RSS feed in iTunes that provides you PDF content.  For me that was Make Magazine, Beatweek magazine, and premium content from Manager Tools.
2. Then hook your iPad to your computer and do a Sync.  After the sync is done, go to the iPad icon in iTunes and select the Podcasts tab and make sure your iPad is syncing to the RSS feed content. If the feed like Beatweek is selected in the Podcasts tab you won't see anything in the Episode list since a PDF isn't according to Apple a media format like MP3 or MOV.
3. Now go to the the Books tab on the iPad and check Sync Books.  Depending on your preference you can select All Books or Select Books to sync.  I used Select Books and then checked the books I wanted.
4. Then you can do a Sync and your PDF's will be in the iBooks applications on the iPad.

I did notice two "bugs" or "issues".  The first, only PDFs that appear to be listed in the Books Selection area in iTunes are PDFs that have been downloaded since iTunes 9.2 was released.  I haven't been able to seamless get older PDFs to load in this manner. The second, the feeds now show up in your Podcast list in iTunes.  If you go to a podcast feed with PDF files, the PDFs are listed there (–:–), and if you click on them the screen goes blank trying to play them like an audio or video file.  Just tap once and you should be able to exit out.

Before this option, I have been successfully using GoodReader for PDFs reading, but this new iBook method is pretty compelling as it can be setup to be automatic.  These two bugs are pretty distracting though, and hopefully they will get addressed soon.

Thoughts? Comments? Let me know!