From a diagram posted in another question on this site, it looks as if WinRT will sit side-by-side with .NET and Win32, i.e it is an alternative rather than a replacement.
I think the idea is that WinRT will be used for small apps that are suitable for tablet based PC's, but will also be available under Desktop Win8 so these systems can also use the same apps.
Applications specifically designed for Desktop Win8, such Visual Studio, Office, Photoshop etc. will still continue to use .NET or Win32.
If you need your app to be portable and work on tablets and Desktops, then WinRT is for you. If you only intend for your app to be used on desktops, then Win32 or .NET are your options. (This is assuming that WinRT is less powerful than existing technologies, if this is not the case, then WinRT becomes a no-brainer).