I simply wondered whether people thought it was worth learning to use the MSBuild syntax in order to customise the build process for a .net project, or whether it is really not
MSBuild is definitely worth learning for anyone and everyone writing .NET software. The reason a build server for .NET apps no longer requires Visual Studio to be installed (as Andrew Burns mentioned) is because MSBuild is part of the .NET Framework now.
Knowing MSBuild will give you significant flexibility in choosing what technologies you use to implement continuous integration. Because I took the time to learn MSBuild, I was able to change the CI system one of our teams was using from CruiseControl.NET to TeamCity without much difficulty. Those CI servers, or something like FinalBuilder (which I'm not familiar with), are better options for performing nightly builds than a scheduled task. Learning how to implement custom MSBuild tasks will give you even more flexibility in implementing custom builds. Jivko Petiov listed a number of tasks that MSBuild makes easier. In the case of database deployment and configuration, I've written scripts that do this in MSBuild, and it makes the development and testing process much easier.
If Visual Studio Team System is in your future, applications built using MSBuild will be much easier to move into that environment than those built via alternative means.
There are a lot of resources available to help you get started with MSBuild. I'd start with Inside the Microsoft Build Engine. One of the co-authors also has a ton of stuff on the web, including this site, and a project on CodePlex.