As a training/check and line Captain, here is my perspective...
On flights that are not training (ie, most line flights), I do not in any way interfere with the First Officer when he is the PF, and generally the operation goes very smoothly. However, there can be occasions when the Captain sees a situation developing, of which the F/O is not aware, and in these cases the Captain has a responsibility to speak up....diplomatically is the preferred method, otherwise the comments can be construed as "interferring", and sometimes are not well received.
First Officers must remember however that the Captain is assigned to the flight as the Commander (ie, ultimate responsibility) and the company/regulatory authorities will hold him liable in the event of an incident.