Yes, MBI started on an open platform (RepRap), then created proprietary aspects that they think give them a competitive advantage.
Most of them are minor, such as adding a bi-stable lever to the spring-tensioned extruder. But they didn't attempt to patent the community designs.
Most of the people freaking out are badly misreading the patents. That's not too surprising, since patents are pretty hard to read. But the parts where people are claiming MBI is patenting community designs are actually where MBI is documenting the prior art, which is exactly the opposite - they're documenting other people's designs because that's precisely what they're supposed to do, and they're not claiming those designs for MBI.
Don't propagate a misreading of the patents.
And MBI didn't "take" community ideas - everything that was open is still open, and MBI has contributed to open projects, and even started some open projects (e.g. Conveyor, Miracle Grue). And they strongly support open, shared designs, where they host hundreds of thousands of designs on Thingiverse for free.
MBI has been saying for years that they're making tools that are used by Makers, much like (for example) Epilog laser cutters. They don't feel that you can grow a large hardware company on purely open designs, because a competitor can come in that does no R&D and charge only for raw hardware costs and undercut on price, making the industry a "race to the bottom". So they keep open what they feel they can, and they keep closed the parts that they think protect them from "clones". You may disagree with their assessment, but they're being consistent.
As evidence that MBI might be right, there are several Chinese companies that took their open Replicator designs and crank out cheap copies, basically relying on MBI's design and software investments and selling at pure hardware cost. They're limited (legally) to using MBI's older designs, while MBI is attempting to innovate, and patent the innovations, to stay ahead of the cheap clones. And (amusingly) at least one of those cloner companies has now made enhancements to MBI's designs, and kept those enhancements proprietary, probably because they want a competitive advantage against smaller cloner^2 companies.
So you might prefer that MBI had stayed 100% open, and that's a reasonable discussion. There are certainly (smaller) companies that are purely open, and you'd perhaps be happier being their customer because you support that decision.
But when you make false accusations against MBI, instead of sticking to the facts, then it undermines your whole case.