We saw the same thing once CDs and PCs started spreading. The introduction of mp3s where thought of as a threat to the music industry so they fought hard to scare people or make it illegal. In the end the people won out. Some companies still try to lock the music file down but when most people are buying the DRM-free versions, there is not much else they can do without losing all their customers and shutting down the business.
Right now the same type of battle is brewing over movies, and we are only seeing the first minor scratches in the surface in the ebook world. It will be at least another 5-20 years before the dust settles and a single major format that everyone accepts will become the norm, but the individual companies will still have their proprietary formats around for a while (like Amazons AZW). I suspect it will start with something like a Google eReader with a linux inspired open source OS and file format that catches on like wildfire.
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