One of the problems with BIDS is that it wont allow you to have folders and subfolders. You can have a project for each folder which will the do the trick for single level hierarchies.
You can create a simple folder structure and load that into GIT, however then you cant use the Visual Studio editor..
So what I've done is create a solution that has 2 project in it.
One is an empty C# project that contains the folder structure for SSRS and the other an Actual SSRS project.
Both are connected into GIT.
The only downside here is in order to use the BIDS editor you need to import the report.