There is a strong perception (whether accurate or not--and I honestly don't know the answer) that it's the same old story with Microsoft: if you go the .NET route, you've gotta buy into the entire Microsoft ecosystem. It's not just .NET that you're choosing; you're also choosing Windows servers, IIS, Visual Studio, etc. If that perception is accurate, it's entirely reasonable to say, "Despite liking a lot of what .NE…
What's interesting is this perception is exactly why the medium-sized company I work for uses .NET. They pay big money for the MS support. So they are reluctant to use other non-MS product because of the cost and risk of introducing another place to go to for support. The other big issue for them is licensing.