It's a little harsh to compare Adobe to Microsoft. They were friendly to the open source community by open sourcing Flex. And as far as controlling the runtime goes, that does have some risks going forward as you say, but it also has the benefit of allowing cross-platform web development largely free of browser-compatibility issues. Which is nice.
At least with Java, you had multiple working implementations of the VM from multiple vendors. With the Flash VM, there's only Adobe's VM, and they've made no indications of opening the code anytime soon.
