You could also use the following in the Python Console to change all expressions of each rule to $id = $atlasfeatureid:

layer = qgis.utils.iface.activeLayer()
renderer = layer.rendererV2()
for rule in renderer.rootRule().children():
    rule.setFilterExpression('$id = $atlasfeatureid')

Edit:

The above code replaces all expressions entirely. However, if you want to add another expression to an existing one, you can use:

layer = qgis.utils.iface.activeLayer()
renderer = layer.rendererV2()
for rule in renderer.rootRule().children():
    rule.setFilterExpression(rule.filterExpression() + 'AND $id = $atlasfeatureid')

You could also use the following in the Python Console to change all expressions of each rule to $id = $atlasfeatureid:

layer = qgis.utils.iface.activeLayer()
renderer = layer.rendererV2()
for rule in renderer.rootRule().children():
    rule.setFilterExpression('$id = $atlasfeatureid')

Edit:

The above code replaces all expressions entirely. However, if you want to add another expression to an existing one, you can use:

layer = qgis.utils.iface.activeLayer()
renderer = layer.rendererV2()
for rule in renderer.rootRule().children():
    rule.setFilterExpression('({}) AND $id = $atlasfeatureid'.format(rule.filterExpression()))

You could also use the following in the Python Console to change all expressions of each rule to $id = $atlasfeatureid:

layer = qgis.utils.iface.activeLayer()
renderer = layer.rendererV2()
for rule in renderer.rootRule().children():
    rule.setFilterExpression('$id = $atlasfeatureid')

You could also use the following in the Python Console to change all expressions of each rule to $id = $atlasfeatureid:

layer = qgis.utils.iface.activeLayer()
renderer = layer.rendererV2()
for rule in renderer.rootRule().children():
    rule.setFilterExpression('$id = $atlasfeatureid')

Edit:

The above code replaces all expressions entirely. However, if you want to add another expression to an existing one, you can use:

layer = qgis.utils.iface.activeLayer()
renderer = layer.rendererV2()
for rule in renderer.rootRule().children():
    rule.setFilterExpression(rule.filterExpression() + 'AND $id = $atlasfeatureid')