First of all, when Yahoo, Google or any large company acquires a product, they don't necessarily do it for the product, but possibly for other technology. The goals of the acquiring company, the founders and the users are not necessarily aligned. This doesn’t mean the acquisition is bad for the company or founder, just bad for the users of the product or possibly for the founders if it goes in a direction he or she didn't like.
Second of all, founders leave for all sorts of reasons. It seems like some of these founders were frustrated by Yahoo!, but I have a feeling that founders in general would be frustrated by working for anyone in general. There's a personality that starts companies and there’s a personality that works for them.