I think the disconnect here is that its not unreasonable, illegal, or even particularly surprising that a company like Makerbot might seek these patents, especially in light of their acquisition.

Our (the makers) problem is that it was rude. The community supported them in large part because of their declared support of openness. What they're doing isn't like running a red light because they're in a hurry, its more like farting on an elevator. The backlash is justified.