I think bundling a free copy/discounted copy of the ebook with a regular priced physical book is a great idea for the reader. And if you think about it, not really that bad for the author as well. The people that are going to purchase the physical book are not likely to also purchase the full price ebook of the exact same book, so to say that the author is missing out on royalties seems incorrect in my opinion. The person was never going to buy the ebook anyway, only the physical book. Buying both full price would seem terribly uneconomical. But think of the added convenience for a person who much prefers a physical book, but also likes the convenience of an ebook and has a nook/kindle/ipad/smartphone. Lets take Stephen King's Under The Dome for example. It's a huge book, a massive book. I love physical books, and much prefer them to ebooks, but I must say, it sure would have been easier and more convenient to have read UTD on my Nook, and been able to simply slip the slim, lightweight device into my laptop bag when I went to work, or the coffee shop, or where ever, instead of trying to lug around and read the mini-fridge that was UTD. I would have never chosen only the ebook, because I love my physical books, and they are about the only thing I collect, but if the ebook had been bundled free, or, yes, even heavily discounted, with the physical book at purchase,I would have done a good chunk of my reading on the ebook edition. And lets face it, Free is not going to happen, and I understand that. But I think even discounted ebooks as a bundle with the physical book people would go for.
Let the publishers/bookstores figure out the sales figures / royalties with this, but I think its a win for the readers, and if done correctly could be win for the publishers/authors as well.