I am no expert but I believe Stratasys paid for the brand and community. MakerBot is the most well-known 3D printer out there but not the cheapest or most well-designed (in the prosumer category). My guess is that the infusion of cash will help MakerBot manufacture more printers at cheaper costs and, thus, enable them to target additional market segments (beyond the prosumer category, where they already face competition from Form1 labs).
Also, Bre Pettis has a lot of supporters who'll stand by him no matter how self-serving his actions. For example, people supported him using his blog to to publicly humiliate newbies to Open Hardware for not opening up their derivatives of his designs sufficiently. The same people later insisted there's nothing wrong with him closing off his derivatives of other's designs and that anyone who complains about this is hostile and inflammatory, even comparing them to terrorists - because of course, holding someone to the same standard they hold others to is far less inflammatory than calling someone a terrorist fundamentalist. I am sadly not kidding.
Edit: I wouldn't even be surprised if Stratasys managed to get away with patent lawsuits against open 3D printer manufacturers with him on board.
