First off, it is always bad to fear things that cannot be controlled. Physibles (data objects that can become physical objects) will become a reality on some level. If it ends up being possible and prevalent to print running shoes, piracy prevention measures will likely be as effective as DRM has been for music and movies. So let's all just calm down about how to stop the technology and think about how to use it.
Second, there isn't much of a reason for manufacturers to fear this new technology. It is crazy to think that it will be cheaper and easier for most users to print a product at home instead of buying it and having it delivered. The best kind of profit to be made is from leveraging high volumes to bring down prices and complexity, then using that margin to recoup development costs. That business model is the reason that electronics manufacturers used to publish full service manuals containing schematics without fear of being undercut. This practice is largely hindered due to increasing costs and the vulnerability from off-shore manufacturers copying the design and competing with the same volumes at lower costs (a big problem, but not related to physibles).
There are, however, some manufacturers that should be shaking in their boots at the notion of people printing parts at home. Companies that try to turn inexpensive ABS plastic parts into a profit center by charging huge margins are all too common. When these companies find their oversized margins demolished by physibles, they can only blame their demise on the fact that they decoupled their income sources from the value they bring to customers.
The last reason manufacturers should not fear physibles is the position of power that they currently hold – a truly unique situation in a truly unique time. They have the benefit of hindsight from how piracy affected the music and movie industry. Media companies tried desperately to hold on to their high-margin boxed media products even though it went against the grain of what the customer really wanted. This only drove potential customers to piracy as the only means of downloading content.
Now that the digital media dust is settling, companies are finding that there is a large market for digital media that competes on convenience, legal, and moral grounds. But since they left it to others to create an online store offering digital media when the market emerged, Apple and Netflix take a (rather large) piece of the pie. Compare that to where part manufacturers are today. They have the technical drawings, staff, and revenue that can be used to develop a way to offer part information to their customers directly. Selling the physible in an easy, legal, and reasonably priced way while 3D printing technology develops would be revolutionary. The 'factory-direct' approach could allow them to have a price low enough to compete with the free, illegal, and less convenient Pirate Bay. There will certainly be pirates copying the design for free, but it may end up having the same impact shoplifters have on stores; unfortunate, but tolerable.
As with most disruptive technologies, approaching physibles with fear can only be good in the short term. Hopefully the people working hard to invent the next great widget will be paid for the value they create, even if on a totally different business model.