If you want to deploy .NET 4 to Servers running Server Core operating system you will need to download the .NET 4 standalone installer for Server Core. You can download this file from the link below.
Here is a screenshot of a basic PDQ Deploy Installer which will install .NET 4 on a Server Core system. Note that this screenshot is taken from PDQ Deploy 2.0.
If you are deploying to Server 2008 R2 Server Core then you need to verify that WoW 64 as well as .NET 2.0 are installed. To install from the command line you would run
Dism /online /Enable-Feature /FeatureName:ServerCore-WOW64
Dism /online /Enable-Feature /FeatureName:NetFx2-ServerCore
Dism /online /Enable-Feature /FeatureName:NetFx2-ServerCore-WOW64
If you are running PDQ Deploy in Pro Mode you can create Command Steps to enable these features and then have a Package Step to install .NET 4.