from PyQt4.QtCore import Qt

for layer in QgsMapLayerRegistry.instance().mapLayers().values():
    renderer  = layer.rendererV2()
    if renderer.type() == 'RuleRenderer':
        ltl = QgsProject.instance().layerTreeRoot().findLayer(layer.id())
        ltm = iface.layerTreeView().model()
        legendNodes = ltm.layerLegendNodes(ltl)
        for ln in legendNodes:
            ln.setData(Qt.Unchecked, Qt.CheckStateRole)
            #ln.setData(Qt.Checked, Qt.CheckStateRole)