The reason is that the .NET Framework 3.5 delivers not whole new runtime machine, but only library extension of .NET 2.0. In other words there are no new CLR or new language compilers. But there are new available libraries and new versions of C# (3.0) and VB (9)
.NET Framework 2.0 includes the CLR, Winforms, Asp.NET and web services.
.NET Framework 3.0 includes in addition libries for WCF (Windows Communication Foundation), WPF (Windows Presentation Foundation) and Windows Workflow (WF).
.NET Framework 3.0 includes in addition libraries for AJAX, LINQ and REST
Finally you will see there is no problem with your IIS. You've just received some new additional and really good features for easier programming.