I had this problem too, I had created a new empty C++ project. then created my src folder and started adding classes and folders as normal. The solution i found was to set up the C++ include paths.
For those who do not know how to do that what i did was : make sure your open project is selected in eclipse go to : "project" > "properties" > "C/C++ Build" > "Settings"
Then add include paths within "GCC C++ Compiler" > "Includes"
I am using workspace relative paths so i need this entry to exist: "${workspace_loc:/${ProjName}/src}"
Then beyond that add any other folders you need to access header files within.