The biggest con is not having a professionally bound book, in front of you, that you can page back and forth through. You lose the feel of the pages, the smell of printers ink and good paper pulp (rather than the steril computer paper you get when you print it out), and the overall feel that this is a lasting thing, a book that will go on public and private library shelves and be paged through by perhaps another generation. In other words...you lose its bookishness, which is a wonderous and powerful thing. How many of us would be playing this game if we were not enamoured with books when we were younger?
You cannot resell a pdf file. You will never dig it out of a dusty bin in a used book store, or admire it at an auction.
It will never be something your nongaming friends see on your shelf and inquire about. It will not be there when you glance over at your gaming material, ready to inspire a new idea, merely because it stands out in your mind as an image of a complete work as opposed to a few electronic words.
You will not take it with you to your gaming sessions, or to browse while in the bathroom, or while on vacation, unless you print it out or carry a laptop.
You will not be able to flip through the pages before you buy it at your local gaming store.
You will not support your local gaming store in buying it, spelling potential doom for the industry as new entry into the hobby becomes more and more difficult from lack of exposure at such stores.
You will make it all that much easier for people to steal it. If you doubt this, ask yourself how many people download mp3s without permission, compared to how many steal it from a music store. And then ask yourself if you have ever known a gamer who would download it, given the opportunity.
If your computer ever crashes, gets infected by a virus, or gets corrupted files, you may very well lose the pdf forever.
There are a few more "cons" to pdf books.