To provide multiple paths in the CMAKE_PREFIX_PATH variable you need to delimit each entry by ;(semicolon). So your command will look like:
cmake -DCMAKE_PREFIX_PATH="C:\Qt\5.5\msvc2013\lib\cmake;C:\protobuf\src;C:\protobuf\cmake\build\Release"
To check if everything alright with the provided paths you can use the following code in the cmake file:
foreach(path ${CMAKE_PREFIX_PATH})
message("Path: " ${path})
endforeach(path)
It will print every path provided.