The reasons things happen in government rarely are for what's stated publicly. The real reasons are buying votes, getting campaign contributions, rewarding friends, giving preferential treatment to one group in exchange for something else, or simply political posturing.
The FAA is getting something. I was thinking about this last night, and the only thing I can come up with now is what Formstone alluded to. This registration is the first step. The second or third is to restrict hobby flying to fields designated for such. The Amazon angle sounds far-fetched, but isn't out of the question if other businesses get into using drones. That would be a very plausible reason for this registration.
The internet sales tax bill has been slowly but steadily advancing in Congress. The single biggest lobbyist for the legislation is Amazon, as they know it will drive small internet retailers out of business.