Several reasons.
Obviously, part of it is money. A unit sold through a counterfeiter instead of one built by Bowling & Grippo or licensed from them is money B&G and their authorized distributors won't get. And these counterfeiters I'm talking about are commercial operations, not somebody who's made a couple one-offs in his basement for personal use.
Second reason is they put a drain on support that is financed by the above sales. There have been quite a few times people bought a counterfeit ECU and came to me for support, or posted on the MegaSquirt forums trying to get help they couldn't get from the original seller (which are paid for out of the Bowling & Grippo budget).
Third reason is quality. There have been several very poorly done MegaSquirt ripoffs - one that comes to mind is the now defunct Fuel Injection Pro, who built a lot of ECUs for the Starion / Conquest community. Whoever laid out their board had no idea how to size PCB traces. I've personally seen two of their ECUs (and been emailed pictures of several more) with the exact same burned point on the injector control trace because it is way too thin to carry serious amounts of current. Poorly made knock offs can give a correctly designed original a bad reputation if people don't realize they are fakes.