MSBuild being integrated with Visual Studio gives programmers less friction to use the build system. It mainly comes down to them only having to go "Build Solution" and it all works, versus having to use Custom Build Steps and other such things, or, worse, forcing developers to build by launching some kind of external script.
Now, I mostly tend to prefer MSBuild over NAnt because it's simpler. Sure, NAnt has a lot more features, is more powerful, etc., but it can quickly get out of hand. If you and your build engineers have the discipline to keep the NAnt scripts simple, then it's all good. However, I've seen too many NAnt-based systems go south to a point where nobody understands what it's doing anymore, and there's no real way to debug it besides doing the equivalent of a good ol' printf. The moment you start using some if/else statement or for loop, that's where, IMHO, it starts smelling.
On the other hand, MSBuild has a solid foundation based on metadata and a less verbose syntax. Its simplicity (or lack of features... depending on how you see it) forces you to write logic in .NET code via new tasks, instead of writing logic in XML markup. This encourages re-usability and, above all things, lets you actually debug your build system in a real debugger.
The only problem with MSBuild is the not-so-occasional bug (especially in the first version) or obscure (although documented) behaviour. And, if that's the kind of thing that really bothers you, being tied to Microsoft.