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Condensing comments into an answer:
When you make a Marker visualization_msg and you want to visualize Points there is a difference between the marker's position and the point's position. The markers positions is specified by a pose and a frame_id which essentially describes in the 3D world where the marker object will be placed. The marker object itself contains an array of points each specified by a position, which is measured relative the origin of the marker object.
Therefore in order to visualize a Marker containing Points, you need to specify the pose of the Marker itself, and then the location of the Points within that marker object.
See the comments for two links which are better understood in context in-situ.
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