JSON formatting and processing hierarchies
Assuming you're using JavaScript to manipulate the object, you could also split it up into 2 different structures, one for maintaining the hierarchy and another for easy access:

var hierarchy = {
    transportation: {
        road: {
            colour: "rgb(0,0,0)"
        },
        railway: {
            colour: "rgb(100,100,100)"
        }
    }
};




var features = {
    road: hierarchy.transportation.road,
    railway: hierarchy.transportation.railway
};