It's easy to say that now, but time has a funny way of winkling out deeply seated truths that we try to shy away from. Trust me, I like the CLR, I used to work in DevDiv, it's close to my heart.
However, one has to wonder if something is missing or not quite right. The CLR was originally a grand strategic play. It was intended to be everywhere, in Windows, in browsers, in game consoles, in phones, everywhere. And not just present everywhere but also underpinning all of these important products. A lot of the big projects to convert native code to managed code, such as in Windows, foundered and failed. Other than Microsoft.com most of the rest of Microsoft compiles their products to native code. Meanwhile, Windows has released its own "runtime" (WinRT) and windows mobile development is migrating toward native development as well. Not to mention the failure of silverlight to gain traction. The niche the CLR serves today is vastly diminished from the vision even 5 years ago. Also, they've tried to break out of their niche by making sweeping improvements to the CLR such as adding dynamic language support and such-like but they still seem to be stuck in the same rut as ever.
Maybe the CLR will stick around forever, but given the trends it's looking increasingly likely that in, say, 10 years the CLR will be a bit like vb6. Still supported by default in every windows release but no longer fully embraced by the current tool chain.