> Venture-backed companies are generally forced to file patents -- often very silly and overbroad ones -- by their investors, who are alive to the possibility of flogging them off to a troll in the (likely) event that the company fails.
If you're dealing with an R&D focused company, as opposed to a product company, it is essential for investors to require the company to take out patents. Without a patent, an R&D focused company is an empty shell with no assets. All the technology is in a bunch of engineers' brains, all of whom can walk out the door at any moment. If the company isn't successful, without a patent investors are left with no assets of value, even if they produced technology that is itself valuable. Competitors can come along and hire away the engineers or just pick through the publications to glean the benefit of the R&D that the investors may have poured tens of millions of dollars into. And this is also where NPE's show their value: if investors can count on being able to sell the technology to an NPE who might then try and license it out, they are more likely to be willing to invest in the first place.
For a company like Makerbot, patents are going to be essential. Their brand isn't worth anything. They don't have an audience of users that might be disinclined to use a competitor for loss of the network effect. They've got technology, which by virtue of their generally open nature, is easy for a competitor to copy without the R&D effort they had to put into developing the technology in the first place. And as far as I can tell, they're not running a non-profit and have been the subject of tens of millions of dollars in investment.